bluuebunny/crossref_metadata_2025 huggingface dataset:
Peptide profiling of goat milk fermented by Lactobacillus delbrueckii ssp. delbrueckii BD7: Identification of potential biological activity
Authors: Rubak Yuliana Tandi , Nuraida Lilis , Iswantini Dyah , Prangdimurti Endang , Sanam Maxs Urias Ebenhaizar
Published: August 2021

Abstract. Rubak YT, Nuraida L, Iswantini D, Prangdimurti E, Sanam MUE. 2021. Peptide profiling of goat milk fermented by Lactobacillus delbrueckii ssp. delbrueckii BD7: Identification of potential biological activity. Biodiversitas 22: 3136-3145. This study investigated the angiotensin-converting enzyme (ACE) inhibitory activity in fermented goat milk by Lactobacillus delbrueckii ssp. delbrueckii BD7, characterizing the peptide and its potential as a bioactive peptide. The starter culture (2%) was inoculated into pasteurized goat skim milk (11%), then incubated at 37 °C until it reached pH 4.6. Centrifugation at 6000 g x 10 minutes at 4 °C was applied. The supernatant obtained was then ultrafiltrated using a membrane cut-off with a molecular weight of 3 kDa, and the fraction obtained was analyzed to determine the inhibitory activity of ACE. Peptides were characterized using Nano LC / MS / MS, and identification as bioactive peptides was carried out based on a literature review. ACE inhibitory activity of fermented goat milk of Lb. delbrueckii ssp. delbrueckii BD7 was 55.98 ± 3.53%. A total of 157 peptides were released with molecular weights ranging from 770.78 - 2081.12 Da and having 7-19 amino acid residues. The main peptide was hydrolyzed from casein (72.6%), cleavage in the parent protein, specific for aliphatic and aromatic amino acids. Identification of bioactive peptides based on the similarity of amino acid residues at C-terminal obtained 28 ACE inhibitor peptides, 19 antioxidant peptides, and ten antimicrobial peptides. Some of these peptides have homologous sequences with previously reported peptides. Lb. delbrueckii ssp. delbrueckii BD7 has the potential as a starter culture to produce fermented milk, which is rich in biological activity.
Ethnobotanical survey and phytochemical screening of anti-snakebite plants used in Bissok District of Gabon
Authors: Mengome Line Edwige , Mewono Ludovic , Mboma Raymonde , Engohang-Ndong Jean , Aboughe Angone Sophie
Published: August 2021

Abstract. Mengome, Mewono L, Mboma R, Engohang-Ndong J, Angone SA. 2021. Ethnobotanical survey and phytochemical screening of anti-snakebite plants used in Bissok District of Gabon. Biodiversitas 22: 3264-3275. Snakebites remain a major health issue in tropical and subtropical regions in the world. The limited access of antivenom sera in remote areas of many countries forces populations to rely on plant-based remedies to manage snakebite-induced injury. In this study, we conducted an ethnobotanical survey of medicinal plants used for the management of snakebites in the district of Bissok (Northern Gabon). After collecting and verifying the authenticity of the plants, we further performed their phytochemical analysis. The procedure used in this study involved a structured questionnaire and direct interviews of local populations. Overall, data collected on-site included local names, the part of the plant used, the preparation, and the route of administration. The presence of some phytochemical compounds was determined according to standard methods. Overall, a total of 29 species of plants belonging to 20 different families were reported to be used to treat snakebites. The plants used were herbs (44.80%), trees (24.10%), shrubs (20.70%), liana (10.30%), and rhizomes (6.90%). They were mainly used as poultice or crush, and to a lesser extent as decoction and maceration. Regarding the route of administration, interviewees reported mainly external use on the site of the bite. Concerning the chemical composition, we found that the antivenom plants were rich in chemical compounds known to have antivenom, antipyretic and antimicrobial properties, e.g. alkaloids, terpenoids, flavonoids, steroids, coumarins, phenols, tannins gallic Our results open avenues to develop venom enzyme inhibitory assays.
Stock status of Nile tilapia (Oreochromis niloticus) in Aneuk Laot Lake, Sabang District, Aceh Province, Indonesia
Authors: Prianto Eko , Purwoko Rudi Masuswo , Kasim Kamaluddin
Published: August 2021

Abstract. Prianto E, Purwoko RM, Kasim K. 2021. Stock status of Nile tilapia (Oreochromis niloticus) in Aneuk Laot Lake, Sabang District, Aceh Province, Indonesia. Biodiversitas 22: 3364-3370. The Nile tilapia (Oreochromis niloticus) fishery in Aneuk Laot Lake plays a vital role in the local livelihoods. There is an indication of the massive exploitation of the species that potentially harm the stock and threaten its sustainability. This research aims to evaluate and assess the Nile Tilapia's stock status and use the results as baseline information to the management authorities. Surveys were conducted from May 2018 to April 2019 by collecting the length-weight data, sex, and gonadal maturity stage of 600 individuals. The Length-Based Spawning Potential Ratio (LB-SPR) was used to determine the Spawning Potential Ratio (SPR) and compared the results to the reference point. The results show that 50% of the females have matured at 15.1 cm, while the males at 17.8 cm. The individual fish length varies from 12.15 to 20.5 cm, whereas 50% of them were caught at size 17.8 cm (Lc50), meaning that predominantly of the fish had experienced first spawning before they were captured. The current SPR is about 5%, confirming the Nile tilapia's stock status is at an unhealthy state. Consequently, the precautionary approach, such as increasing the mesh size and limiting effort, should be considered to ensure the sustainability of the recruitment.
Short Communication: Assessing phytoplankton species structure in trophically different water bodies of South Ural, Russia
Authors: Kostryukova Anastasiya M. , MASHKOVA IRINA , BELOV SERGEY , SHCHELKANOVA ELENA , TROFIMENKO VIKTOR
Published: August 2021

Abstract. Kostryukova A, Mashkova I, Belov S, Shchelkanova E, Trofimenko V. 2021. Short Communication: Assessing phytoplankton species structure in trophically different water bodies of South Ural, Russia. Biodiversitas 22: 3530-3538. The study aims to analyze the species structure of the phytoplankton communities of four water bodies in South Ural (Lakes-Turgoyak, Uvildy, Ilmenskoe and Shershnevskoe reservoir). These water bodies are characterized by different trophic states and levels of anthropogenic impact. Lake Turgoyak is oligotrophic; Lake Uvildy is oligomesotrophic. Both water bodies are protected areas and natural monuments. But tourism and recreation are not prohibited on their territories. The mesoeutrophic Lake Ilmenskoe is partially located within the Ilmen State Reserve, and it experiences less anthropogenic impact. The eutrophic Shershnevskoe reservoir is located within the boundaries of the city of Chelyabinsk. It is used as a source of drinking water. Cyanobacteria was the dominant division in the eutrophic Shershnevskoe reservoir. Bacillariophyta dominated in the plankton communities in oligotrophic Lake Turgoyak and oligomesotrophic Lake Uvildy. Green and blue-green algae biodiversity increased in the oligomesotrophic Lake Uvildy. For the mesoeutrophic Lake Ilmenskoe, diatom algae are dominant, but a higher proportion of Chlorophyta (especially Cyanobacteria) was revealed. Species similarity among phytoplankton communities in the given lakes was studied through cluster analysis based on the Sorensen-Czekanowski coefficient. The higher level of similarity between plankton species compositions could be explained by their locality rather than their trophic status.
Prevalence of Argulus indicus, histopathology and hematological properties of infected wild fish in Lake Towuti, Indonesia
Authors: Amriana Amriana , Sari Kesuma D. , Sriwulan Sriwulan , Anshary Hilal
Published: August 2021

Abstract. Amriana, Sari DK, Sriwulan, Anshary H. 2021. Prevalence of Argulus indicus, histopathology and hematological properties of infected wild fish in Lake Towuti, Indonesia. Biodiversitas 22: 3578-3584. Parasites are disease agents that can threaten the health and survival of wild fish as individuals and at a population level. This study aimed to improve knowledge on the prevalence of Argulus indicus, infestation rates and the pathological effects of parasite infestation on hosts as well as hematological properties of infected fish. This study can inform future studies on the prevention and control of the cases of Argulus indicus infestation. Fish from Lake Towuti (20 45? 0? S, 1210 30? 0? E) were caught from February to May 2019 using traps and gill nets. The total of 373 specimens obtained comprised 102 climbing perch (Anabas testudineus), 74 three-spot cichlids (Cichlasoma trimaculatum), 84 Nile tilapia (Oreochromis niloticus), and 113 striped snakeheads (Channa striata). The prevalence, mean intensity and abundance of A. indicus were highest in C. striata with a prevalence of 81%, mean intensity of 5.17 parasites/fish and abundance of 4.06 parasites/fish. The lowest parasite infection level was seen in C. trimaculatum with a prevalence of 4.1%, mean intensity 1.66 and mean abundance of 0.06. Histological analysis showed inflammatory responses in the skin of snakeheads (hemorrhage, increased spread of melanomacrophage and leukocyte cells), melanomacrophage and the spread of leukocyte cells were observed in climbing perch. In contrast, melanomacrophage was often observed in tilapia and trimac cichlid. Blood imaging analysis showed significant differences (P <0.05) in the number of leukocytes and percentage of monocyte cells between uninfested fish and those infested with A. indicus.
A single-centre ten-year retrospective cohort study of malignant small bowel obstruction
Authors: Cato LD , Evans T , Ward ST
Published: August 2021

Introduction

Management of malignant small bowel obstruction (mSBO) is challenging. The decision to perform an operation evaluates the perceived chance of success against a patient’s fitness for operation. The aim of this study was to characterise the mSBO patient population in a tertiary UK centre and assess the patient’s treatment pathway including use and effects of palliative surgery, total parenteral nutrition (TPN), Gastrografin and dexamethasone as well as preoperative stratification.

Methods

Patients were included if they had mSBO confirmed on computed tomography imaging due to a primary or metastatic neoplasm. Data were collected on pathway and management, and Cox proportional hazard methods were utilised to observe effects on survival.

Results

Ninety-four patients were included, with 104 inpatient episodes. Mean age was 67.4 (SD 13.7), with 57 (60.6%) females. Most (89.4%) had only one admission for mSBO. Eighty-four (89.4%) patients died over the ten-year period, 18 (17.3%) within 30 days of admission. Fifty patients (53.1%) underwent operative management: 70% bypass, 24% stoma formation and 6% open-close laparotomies. Log rank testing of survival probability analysis was significant (p = 0.00018), with 50% survival probability at 107.32 days for operative management and 47.87 days for non-operative.

Discussion and Conclusion

Operative management forms part of the treatment pathway for a significant proportion of patients with mSBO, offering a survival benefit, though quality of survival is not known. Case selection is good, with few open-close laparotomies. Trials of non-operative interventions such as Gastrografin and dexamethasone are not utilised fully.
Implementation of an acute tonsillitis management protocol within a clinical decisions unit
Authors: Balai E , Bhamra N , Gupta K , Jolly K , Barraclough J
Published: August 2021

Introduction

With tonsillectomy surgery subject to increasingly strict commissioning criteria over the past 20 years in the UK, the total number of admissions for acute tonsillitis has been rising steadily. Multiple single-centre studies have demonstrated how introduction of a standardised management protocol can be effective in improving the delivery of treatment for acute tonsillitis in the emergency department.

Methods

Using a novel approach, we aimed to implement an acute tonsillitis management protocol within a formal clinical decisions unit (CDU) pathway. Following a retrospective baseline audit, we carried out two post-intervention cycles of data collection to assess safety and efficacy.

Results

The median number of initial treatments increased significantly from two of five at baseline, to three of five in both the first (U = 86, p = 0.004) and second (z = 2.959, p = 0.003) audit cycles. Admission rate was reduced from 0.79 to 0.44 in the first cycle, representing a 44.6% relative risk reduction [95% confidence interval (CI) 0.304–1.012; p = 0.0547]. Admission rate remained reduced at 0.48 in the second cycle, with a relative risk reduction of 39.2% compared with baseline (95% CI 0.380–0.972; p = 0.038).

Conclusions

Utilisation of the CDU led to an improvement in the delivery of initial treatment, an extended period of observation and subsequently a greater percentage of patients being discharged. An acute tonsillitis management protocol within a CDU appears to be a safe and effective model and is now standard practice in our hospital.
Hemangioma of First Extensor Compartment of the Wrist– A Rare Case Report
Authors: Ranjan Rajni , Kumar Rakesh , Jeyaraman Madhan , Biswas Sandip , Kumar Akhilesh , Agarwal Garima
Published: August 2021

Introduction: Although upper extremity intramuscular hemangioma is a rare clinical entity, it poses considerable morbidity in the functional needs of an individual. The diagnosis of intramuscular hemangioma poses a diagnostic glitch. The combined radiological and histopathological assessment provides a complete understanding and diagnosis for the same. Every tumor follows an individualized protocol for its management.
Case Report: A 15-year-old female presented with swelling over dorsal aspect of distal 1/3rd right forearm, which was 3 cm away from the articular surface of the right wrist from the past 5 years. There was no history of trauma or infection over the right wrist. Finkelstein’s test was negative, which rule out de Quervain’s tenosynovitis. The movements of the right wrist were unrestricted without any distal neurovascular deficit. MRI of her right wrist and hand suggested the presence of low flow vascular malformation within the musculotendinous junction of APL and EPB muscles. The patient underwent excision biopsy of the hemangiomatous lesion in toto without any neurological complications. No recurrence was noted in the follow-up period for 6 months.
Conclusion: Being a benign vascular tumor, MRI provides the gateway to diagnose intramuscular hemangioma for early intervention to provide better functional results. The choice of definitive treatment for APL and EPB hemangioma was excision biopsy in toto which provided better functional results in our patient.
Keywords: Hemangioma, intramuscular, abductor pollicis longus, extensor pollicis brevis, MRI, excision biopsy.
Mycobacterium tuberculosis Infection of the Spine Secondary to Oxygen – Ozone Therapy for Prolapse Intervertebral Disc: A Scoping Review
Authors: Salaria Amit Kumar , Dhatt Sarvdeep Singh , Kumar Vishal , Neradi Deepak , Sodavarapu Praveen , Kumar Naveen
Published: August 2021

Introduction: Ozone therapy is one of the evolving, yet far from conclusive, alternative minimally invasive treatment option in the management of herniated disc in the cervical and lumbar spine. It causes the decrease in the volume of herniated disc by dehydration.
Case Report: We hereby present the first reported case of Mycobacterium infection of the spine secondary to ozone therapy with the aim to caution the surgeons regarding the complications of intradiscal ozone therapy.
Conclusion: Lack of proper, adequate, and recommended precautions if not taken can inoculate the varied microorganisms into the intradiscal space leading to devastating and unforeseen complications.
Keywords: tuberculosis, ozone therapy, infection.
Integrated sensor with a whispering-gallery mode and surface plasmonic resonance for the enhanced detection of viruses
Authors: Hao Yihua , Guo Zhixiong
Published: August 2021

Surface plasmonic resonance (SPR) is integrated into a whispering-gallery mode (WGM) optical microsensor to augment sensitivity in this study. The performance of such WGM silica ring sensors of 20 µm in size with an Ag or Au metal core was evaluated for detection of small respiratory viruses such as COVID-19 via the finite-element modeling. Compared with pure WGM sensors, the integration with SPR enhances sensitivity by 3–5 times and facilitates combination with the polymerase chain reaction method to achieve fast, accurate, and specific virus detection. The presence of a single respiratory virus of 70 to 100 nm in diameter in air environment could shift the sensor resonance wavelength by 36 to 64 pm in the case of an Au metal core or by 34 to 63 pm of an Ag metal core. With use of a general-purpose optical analyzer of 10 pm resolution, a single airborne virus of 20 nm in size is detectable using the proposed hybrid sensor. This corresponds to about 0.005 vol. %. For viruses in aqueous solution, the detection limit rises to about 0.2 vol. %. A fundamental enhancement factor based on relative electric energy ratio is introduced and defined to analyze and quantify sensitivity enhancement for the first time, to the best of our knowledge.
Efficient silicon-based higher-order mode converters based on subwavelength grating slots
Authors: Liang Yi , Xu Yin , Dong Yue , Zhang Bo , Ni Yi
Published: August 2021

Higher-order mode conversion plays a vital role in on-chip multimode applications. Here, we propose an efficient silicon-based higher-order mode conversion scheme that can achieve the mode-order conversion from

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E

0

to

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E

1

(

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E

0

−

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1

) mode and from

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E

0

to

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E

2

(

T
E

0

−

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E

2

) mode, respectively. These mode conversion functions are realized by etching subwavelength grating (SWG) slots on a silicon waveguide, where the design of the SWG slot pattern matches with the required

T
E

1

(

T
E

2

) higher-order mode. According to the calculations, the mode conversion length is only 3.3 µm (4.32 µm) with the mode conversion efficiency (CE) 92.1% (95.6%), mode crosstalk (CT)

−

17.5

d
B

(

−

16.7

d
B

), and insertion loss 0.65 dB (0.5 dB) for the

T
E

0

−

T
E

1

(

T
E

0

−

T
E

2

) mode converter at

λ
=

1.55

µ

m

. Moreover, device bandwidths over 110 nm (

C
E

>

90

%

and

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T

<
−

15

d
B

) and other higher-order mode conversions can also be achieved using the proposed scheme (e.g.,  

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E

0

−

T
E

3

and

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E

0

−

T
E

4

mode converters). We believe such a device scheme would help increase the transmission capacity of on-chip multimode multiplexing transmissions by leveraging more mode channels.
Light-matter interaction in complex photonics systems: introduction
Authors: Agio Mario , Jiang Xunya , Kafesaki Maria , Koschny Thomas
Published: August 2021

This feature issue presents original work on light-matter interaction in complex photonics systems, which has been a continuously growing area of optics and photonics, in terms of both importance and breadth. From disordered systems to highly controlled micro- and nanostructures, recent decades have witnessed the onset of random media, photonic crystals, metamaterials, plasmonics, and, more recently, metasurfaces.
Fresnel diffraction from sector apertures
Authors: Socratovich Batoroev Anatoly
Published: August 2021

The derivation of the analytic representation of the diffraction field from the sector aperture in the Fresnel zone is presented. The new solution is expressed in the form of a convergent series on incomplete cylindrical functions in the Poisson form that makes it possible to calculate and obtain three-dimensional patterns of the field amplitude in the whole image plane. The obtained patterns correspond to the Fresnel approximation and are true for arbitrary values of the opening angle and for the radius of sectoral aperture.
Imaging through dynamical scattering media by two-photon absorption detectors
Authors: Liu Wei , Zhou Zhihao , Chen Lei , Luo Xin , Liu Yuehan , Chen Xianfeng , Wan Wenjie
Published: August 2021

Imaging through a dynamical opaque scattering medium is an almost impossible task, where strong multiple light scattering from moving scatters dynamically prevents imaging formations even with state-of-art techniques like correlation imaging or adaptive optics. Meanwhile, a small number of ballistic photons can still penetrate through but require demanding detection in terms of a ultrashort time gate and high sensitivity. However, visible light is strongly scattered for most of scattering media. Here we experimentally demonstrate a non-invasive coherent imaging scheme based on two-photon absorption capable of imaging through dynamical scattering media with a length equivalent to 28 times mean free paths for single photon transport, where two-photon absorption in a conventional semiconductor photodetector when phase matching is not required works over a wide bandwidth so it can support a fast time gate down to femtosecond level, short enough to distinguish ballistic photons from scattering background, and allows accessing longer wavelengths for deeper penetration. This technique combined with successful optical coherence tomography may pave a new way for imaging through fog, storm, and rain as well as biomedical imaging applications.
100 kHz CH2O imaging realized by lower speed planar laser-induced fluorescence and deep learning
Authors: Zhang Wei , Dong Xue , Sun Zhiwei , Zhou Bo , Wang Zhenkan , Richter Mattias
Published: August 2021

This paper reports an approach to interpolate planar laser-induced fluorescence (PLIF) images of CH2O between consecutive experimental data by means of computational imaging realized with convolutional neural network (CNN). Such a deep learning based method can achieve higher temporal resolution for 2D visualization of intermediate species in combustion based on high-speed experimental images. The capability of the model was tested for generating 100 kHz PLIF images by interpolating single and multiple PLIF frames into the sequences of experimental images of lower frequencies (50, 33, 25 and 20 kHz). Results show that the prediction indices, including intersection over union (IoU), peak signal to noise ratio (PSNR), structural similarity index (SSIM), and time averaged correlation coefficient at various axial positions could achieve acceptable accuracy. This work sheds light on the utilization of CNN-based models to achieve optical flow computation and image sequence interpolation, also providing an efficient off-line model as an alternative pathway to overcome the experimental challenges of the state-of-the-art ultra-high speed PLIF techniques, e.g., to further increase repetition rate and save data transfer time.
Time-resolved ultrafast laser ablation dynamics of thin film indium tin oxide
Authors: Hallum Goran Erik , Kürschner Dorian , Redka David , Niethammer Dorothée , Schulz Wolfgang , Huber Heinz Paul
Published: August 2021

The interaction of ultrashort laser pulses above the ablation threshold of thin-film indium tin oxide (ITO) is examined with pump-probe microscopy. We are able to observe photomechanical spallation at delay times of hundreds of picoseconds, which plays a stronger role near the ablation threshold of 0.17 J/cm2. A phase explosion may also be observed at tens of picoseconds, playing a stronger role for increasing peak fluences. As one exceeds the material removal efficiency maximum near 0.6 J/cm2, a second spallation is observable in the center of the irradiated spot at a delay time of one nanosecond and corresponds to a crater depth of 50 nanometers. No discernable ridge formation has been observed. We recommend an industrial processing window of at least two pulses per position with a peak fluence between 0.6–1.0 J/cm2.
Stereoscopic high-speed imaging of iron microexplosions and nanoparticle-release
Authors: Li Shen , Sanned David , Huang Jianqing , Berrocal Edouard , Cai Weiwei , Aldén Marcus , Richter Mattias , Li Zhongshan
Published: August 2021

In this work, the combustion behavior of seeded iron particles (d50 = 70 µm) in a laminar diffusion flame was studied in a modified Mckenna flat-flame burner. Two high speed cameras in stereo configuration allowed 3D position and 3D velocity measurements of burning iron particles as well as 3D evaluation of particle microexplosions. Microexplosive processes are important since it can affect both combustion stability and formation of product components. The observed microexplosions happened before particle extinction resulting in change of trajectories, velocities, radiation intensities and fragmentation into smaller particles. It was observed for the first time that fragments of these microexplosions tend to produce planar structures. A frequent release phenomenon was observed during the iron particle combustion using magnified thermal radiation imaging and high-speed shadowgraphy. This release phenomenon was indirectly confirmed with scanning electron microscopy of combust products, revealing multiple cracked particle shells and hollow structures. Black body radiation characteristics was observed indicating the release being in condensed phase and emission spectroscopy identified FeO as intermediate species during combustion. The observed release is believed to mainly consist of iron-oxide nanoparticles formed in the homogenous reaction between vapor iron and oxidizers.
Enhancing the light extraction efficiency for AlGaN-based DUV LEDs with a laterally over-etched p-GaN layer at the top of truncated cones
Authors: Zhang Gai , Shao Hua , Zhang Muyao , Zhao Ziqiang , Chu Chunshuang , Tian Kangkai , Fan Chao , Zhang Yonghui , Zhang Zi-Hui
Published: August 2021

It is known that light extraction efficiency (LEE) for AlGaN-based deep ultraviolet light-emitting didoes (DUV LEDs) can be enhanced by using truncated cone arrays with inclined sidewalls. In this work, the air-cavity-shaped inclined sidewall is applied and the p-GaN layer at the top of the truncated cone is laterally over-etched so that more light escape paths are generated for AlGaN-based DUV LEDs. The experimental results manifest that when compared with DUV LEDs only having the air-cavity-shaped inclined sidewall, the optical power for the DUV LEDs with laterally over-etched p-GaN at the top of the truncated cone is enhanced by 30% without sacrificing the forward bias. It is because the over-etched p-GaN makes little effect on the carrier injection and does not affect the ohmic contact resistance. Moreover, the simulation results show that the truncated cone with laterally over-etched p-GaN layer can enhance the LEE because the reduced p-GaN area can suppress the optical absorption and supplies additional light paths for DUV photos. Then, more light will be reflected into escape cones at the sapphire side.
Performance manipulation of the squeezed coherent light source based on four-wave mixing
Authors: Jin Li
Published: August 2021

We present performance manipulation of the squeezed coherent light source based on four-wave mixing (FWM) in alkaline-earth atoms. We investigate the dynamic response of the system and the spectroscopic feature of lasing generated by resonantly enhanced wave-mixing in coherently prepared system. In this method, the spectral purity and stability of the wave-mixing lasing can be manipulated at will by choosing optimal laser parameters. We also analyze the effect of Langevin noise fluctuations on the system and the relative-intensity noise spectrum of the wave-mixing lasing is well below the standard quantum limit (down to -4.7 dB). This work opens new possibilities for alternative routes to laser stabilization and provides a promising path to realize precision metrology.
Pulse evolution and multi-pulse state of coherently coupled polarization domain walls in a fiber ring laser
Authors: Zhu Xiran , Zhang Bin , Zhao Desheng , Yang Linyong , Liu Shuailin , Hou Jing
Published: August 2021

Pulse evolution and multi-pulse state of coherently coupled polarization domain walls (PDW) is experimentally demonstrated in a novel fiber ring laser. Versatile pulse shapes benefit by wide range moving of PDW in the weakly birefringent fiber. The 8.6 m short-cavity structure is more compact and accessible based on a 976 nm pump with nearly zero negative dispersion (-0.0002 ps2). Besides, multi-pulse patterns such as PDW splitting, harmonic mode-locking, and periodic soliton collision are also observed under larger net negative dispersion (-3.09 ps2) and 151m-longer cavity. This is the first demonstration of coherently coupled PDW in a fiber laser using a bandpass filter and the formation of coherently coupled PDW is ascribed to the BPF’s force filtering.
Quantification of HER2 in COS7 cells using quantum weak measurement
Authors: Li Dongmei , Weng Chaofan , Li Kan , Lin Qiang , Zhang Jingjing , Wang Shuqian , Ruan Yi , Yao Jia
Published: August 2021

A Mach-Zehnder interferometer system based on weak measurement was set up to determinate the concentration variation of molecule by measuring the phase difference change between the two optical paths. The spectrum of the light was recorded to monitor the concentration of trastuzumab (Herceptin), which is a humanised monoclonal antibody, targeted to human epidermal growth factor receptor 2 (HER2). The trastuzumab targeting to HER2 was real-time detected and continuously monitored, the HER2 numbers of COS7 cells on a coverslip was determined at pico-molar level. Our weak measurement enabled method proposes an alternative approach for the concentration detection of molecules, providing a promising functional tool for the quantification of HER2 in cancer cells, possibly promoting fields such as the diagnosis and treatment of cancer.
Diode-pumped 1.15 W linearly polarized single-frequency Yb3+-doped phosphate fiber laser
Authors: Fu Shijie , Zhu Xiushan , Zong Jie , Norwood Robert A. , Peyghambarian Nasser
Published: August 2021

Compact and robust high-power single-frequency laser oscillators are in great demand for some specific applications where narrow-linewidth lasers with extremely low noise are required. In this paper, we report a single-mode-diode-pumped watt-level single-frequency Yb3+-doped phosphate fiber laser at 1050 nm based on an all-fiber distributed Bragg reflector cavity. A maximum output power of 1.15 W with a slope efficiency of 66% was achieved with 18-mm-long 8 wt.% Yb3+-doped phosphate fiber. Stable, single-longitudinal-mode lasing with a spectral linewidth of 9.6 kHz and polarization extinction ratio of ∼30 dB was obtained.
Stable reflective state induced by a disturbed planar texture in surface-treatment-free chiral nematic liquid crystals
Authors: Chen Hui-Yu , Tsao Yu-Chuan , Chang Chin-Hao , Chen Jui Jiun
Published: August 2021

Chiral nematic liquid crystals possess a one-dimensional periodic helical structure and are one of the oldest known materials with the ability of selective reflection of light. Their helix orientation, determining their optical properties, can be changed by a variety of stimuli, and it is also dominated by the surface treatment, ratio of the elastic constants and cell thickness. Here, we present a simple method to realize an angular independence reflective state, induced by a stable disturbed planar texture, in a surface-treatment-free chiral nematic liquid crystal cell. The scattering state caused by the defect-rich focal-conic texture can be electrically tuned to the reflective state from the disturbed planar texture in a very short time, and vice versa. These two optical conditions are both stable states in the null field until the next trigger. We find that the disturbed planar texture in the chiral nematic can provide a 100° viewing angle without reflected wavelength shift. The gray level of the reflected intensity can be tuned via application of the voltage pulses. Moreover, in this work, we discuss the effect of the chiral concentration on stabilizing the disturbed planar texture. When the chiral concentration is higher to induce the blue phases, the change in the texture of the ChNLCs after removing the strong electric field can stop at the disturbed planar texture with high reflectivity. In this work, the optical performance and the bistability based on the disturbed planar texture exhibits great potential for many applications, such as tunable filters, see-through/reflective displays and large-area smart windows.
Photoluminescence of InGaN-based red multiple quantum wells
Authors: Hou Xin , Fan Shaosheng , Iida Daisuke , Mei Yang , Zhang Baoping , Ohkawa Kazuhiro
Published: August 2021

Optical properties of InGaN-based red LED structure, with a blue pre-well, are reported. Two emission peaks located at 445.1 nm (PB) and 617.9 nm (PR) are observed in the PL spectrum, which are induced by a low-In-content blue InGaN single quantum well (SQW) and the red InGaN double quantum wells (DQWs), respectively. The peak shift of PB with increase of excitation energy is very small, which reflects the built-in electric field of PB-related InGaN single QW is remarkably decreased, being attributed to the significant reduction of residual stress in the LED structure. On the other hand, the PR peak showed a larger shift with increase of excitation energy, due to both the screening of built-in electric field and the band filling effect. The electric field in the red wells is caused by the large lattice mismatch between high-In-content red-emitting InGaN and surrounding GaN. In addition, the anomalous temperature dependences of the PR peak are well elucidated by assuming that the red emission comes from quasi-QD structures with deep localized states. The deep localization suppresses efficiently the escape of carriers and then enhances the emission in the red, leading to high internal quantum efficiency (IQE) of 24.03%.
Highly stable multiple-access underwater frequency transfer with terminal phase compensation
Authors: Ren Junwei , Hou Dong , Gao Yefeng , Guo Guangkun , Liu Ke
Published: August 2021

A multiple-access underwater frequency transfer scheme using terminal phase compensation is demonstrated. With this scheme, a highly stable 100 MHz frequency signal was disseminated over a 3 m underwater link for 5000 s. The timing fluctuation and fractional frequency instability were both measured and analyzed. The experimental results show that with the phase compensation technique, the total root-mean-square (RMS) timing fluctuation is about 3 ps, and the fractional frequency instabilities are on the order of

5.9

×

1

0

−
13

at 1 s and

5.3

×

1

0

−
15

at 1000 s. The experiment results indicate that the proposed frequency transfer technique has a potential application of disseminating an atomic clock to multiple terminals.
Polarization-insensitive ultra-short waveguide taper
Authors: Zhang Jingjing , Shi Xiaodong , Zhang Zhaojian , Ma Chao , Chen Xuefeng , Liu Liping , Song Xiaoxian , Zhang Haiting , Yu Yu , Ou Haiyan , Guo Kai , Yang Junbo
Published: August 2021

Waveguide taper, a key component in the photonic integrated circuit (PIC), enables on-chip mode conversion, but large-footprint tapers are detrimental to the PIC, which desires compact and efficient devices. Polarization sensitivity also limits the tapers in the applications involving orthogonal modes. In this work, we design an efficient polarization-insensitive ultra-short MMI-based waveguide taper, through the mode spreading principle and the self-image principle. The proposed taper is 26.3 µm long, one order of magnitude shorter than the standard linear taper. We fabricate the taper, and experimentally demonstrate that it exhibits a high transmission efficiency of

∼

70
%

and a wide 1 dB bandwidth of

>

54

n
m

, for both TE and TM polarizations.
Step-by-step guide to efficient subtomogram averaging of virus-like particles with Dynamo
Authors: Scaramuzza Stefano , Castaño-Díez Daniel
Published: August 2021

Subtomogram averaging (STA) is a powerful image processing technique in electron tomography used to determine the 3D structure of macromolecular complexes in their native environments. It is a fast growing technique with increasing importance in structural biology. The computational aspect of STA is very complex and depends on a large number of variables. We noticed a lack of detailed guides for STA processing. Also, current publications in this field often lack a documentation that is practical enough to reproduce the results with reasonable effort, which is necessary for the scientific community to grow. We therefore provide a complete, detailed, and fully reproducible processing protocol that covers all aspects of particle picking and particle alignment in STA. The command line–based workflow is fully based on the popular Dynamo software for STA. Within this workflow, we also demonstrate how large parts of the processing pipeline can be streamlined and automatized for increased throughput. This protocol is aimed at users on all levels. It can be used for training purposes, or it can serve as basis to design user-specific projects by taking advantage of the flexibility of Dynamo by modifying and expanding the given pipeline. The protocol is successfully validated using the Electron Microscopy Public Image Archive (EMPIAR) database entry 10164 from immature HIV-1 virus-like particles (VLPs) that describe a geometry often seen in electron tomography.
A flexible framework for multi-particle refinement in cryo-electron tomography
Authors: Burt Alister , Gaifas Lorenzo , Dendooven Tom , Gutsche Irina
Published: August 2021

Cryo-electron tomography (cryo-ET) and subtomogram averaging (STA) are increasingly used for macromolecular structure determination in situ. Here, we introduce a set of computational tools and resources designed to enable flexible approaches to STA through increased automation and simplified metadata handling. We create a bidirectional interface between the Dynamo software package and the Warp-Relion-M pipeline, providing a framework for ab initio and geometrical approaches to multiparticle refinement in M. We illustrate the power of working within this framework by applying it to EMPIAR-10164, a publicly available dataset containing immature HIV-1 virus-like particles (VLPs), and a challenging in situ dataset containing chemosensory arrays in bacterial minicells. Additionally, we provide a comprehensive, step-by-step guide to obtaining a 3.4-Å reconstruction from EMPIAR-10164. The guide is hosted on https://teamtomo.org/, a collaborative online platform we establish for sharing knowledge about cryo-ET.
Olfactory perceptual decision-making is biased by motivational state
Authors: Shanahan Laura K. , Bhutani Surabhi , Kahnt Thorsten
Published: August 2021

Growing evidence suggests that internal factors influence how we perceive the world. However, it remains unclear whether and how motivational states, such as hunger and satiety, regulate perceptual decision-making in the olfactory domain. Here, we developed a novel behavioral task involving mixtures of food and nonfood odors (i.e., cinnamon bun and cedar; pizza and pine) to assess olfactory perceptual decision-making in humans. Participants completed the task before and after eating a meal that matched one of the food odors, allowing us to compare perception of meal-matched and non-matched odors across fasted and sated states. We found that participants were less likely to perceive meal-matched, but not non-matched, odors as food dominant in the sated state. Moreover, functional magnetic resonance imaging (fMRI) data revealed neural changes that paralleled these behavioral effects. Namely, odor-evoked fMRI responses in olfactory/limbic brain regions were altered after the meal, such that neural patterns for meal-matched odor pairs were less discriminable and less food-like than their non-matched counterparts. Our findings demonstrate that olfactory perceptual decision-making is biased by motivational state in an odor-specific manner and highlight a potential brain mechanism underlying this adaptive behavior.
Mitigating COVID-19 outbreaks in workplaces and schools by hybrid telecommuting
Authors: Mauras Simon , Cohen-Addad Vincent , Duboc Guillaume , Dupré la Tour Max , Frasca Paolo , Mathieu Claire , Opatowski Lulla , Viennot Laurent
Published: August 2021

The COVID-19 epidemic has forced most countries to impose contact-limiting restrictions at workplaces, universities, schools, and more broadly in our societies. Yet, the effectiveness of these unprecedented interventions in containing the virus spread remain largely unquantified. Here, we develop a simulation study to analyze COVID-19 outbreaks on three real-life contact networks stemming from a workplace, a primary school and a high school in France.

Our study provides a fine-grained analysis of the impact of contact-limiting strategies at workplaces, schools and high schools, including: (1) Rotating strategies, in which workers are evenly split into two shifts that alternate on a daily or weekly basis; and (2) On-Off strategies, where the whole group alternates periods of normal work interactions with complete telecommuting. We model epidemics spread in these different setups using a stochastic discrete-time agent-based transmission model that includes the coronavirus most salient features: super-spreaders, infectious asymptomatic individuals, and pre-symptomatic infectious periods. Our study yields clear results: the ranking of the strategies, based on their ability to mitigate epidemic propagation in the network from a first index case, is the same for all network topologies (workplace, primary school and high school). Namely, from best to worst: Rotating week-by-week, Rotating day-by-day, On-Off week-by-week, and On-Off day-by-day. Moreover, our results show that below a certain threshold for the original local reproduction number R 0 l o c a l within the network (< 1.52 for primary schools, < 1.30 for the workplace, < 1.38 for the high school, and < 1.55 for the random graph), all four strategies efficiently control outbreak by decreasing effective local reproduction number to R 0 l o c a l < 1. These results can provide guidance for public health decisions related to telecommuting.
Review of machine learning methods for RNA secondary structure prediction
Authors: Zhao Qi , Zhao Zheng , Fan Xiaoya , Yuan Zhengwei , Mao Qian , Yao Yudong
Published: August 2021

Secondary structure plays an important role in determining the function of noncoding RNAs. Hence, identifying RNA secondary structures is of great value to research. Computational prediction is a mainstream approach for predicting RNA secondary structure. Unfortunately, even though new methods have been proposed over the past 40 years, the performance of computational prediction methods has stagnated in the last decade. Recently, with the increasing availability of RNA structure data, new methods based on machine learning (ML) technologies, especially deep learning, have alleviated the issue. In this review, we provide a comprehensive overview of RNA secondary structure prediction methods based on ML technologies and a tabularized summary of the most important methods in this field. The current pending challenges in the field of RNA secondary structure prediction and future trends are also discussed.
Average semivariance yields accurate estimates of the fraction of marker-associated genetic variance and heritability in complex trait analyses
Authors: Feldmann Mitchell J. , Piepho Hans-Peter , Bridges William C. , Knapp Steven J.
Published: August 2021

The development of genome-informed methods for identifying quantitative trait loci (QTL) and studying the genetic basis of quantitative variation in natural and experimental populations has been driven by advances in high-throughput genotyping. For many complex traits, the underlying genetic variation is caused by the segregation of one or more ‘large-effect’ loci, in addition to an unknown number of loci with effects below the threshold of statistical detection. The large-effect loci segregating in populations are often necessary but not sufficient for predicting quantitative phenotypes. They are, nevertheless, important enough to warrant deeper study and direct modelling in genomic prediction problems. We explored the accuracy of statistical methods for estimating the fraction of marker-associated genetic variance (p) and heritability (HM2) for large-effect loci underlying complex phenotypes. We found that commonly used statistical methods overestimatepandHM2. The source of the upward bias was traced to inequalities between the expected values of variance components in the numerators and denominators of these parameters. Algebraic solutions for bias-correcting estimates ofpandHM2were found that only depend on the degrees of freedom and are constant for a given study design. We discovered that average semivariance methods, which have heretofore not been used in complex trait analyses, yielded unbiased estimates ofpandHM2, in addition to best linear unbiased predictors of the additive and dominance effects of the underlying loci. The cryptic bias problem described here is unrelated to selection bias, although both cause the overestimation ofpandHM2. The solutions we described are predicted to more accurately describe the contributions of large-effect loci to the genetic variation underlying complex traits of medical, biological, and agricultural importance.
Maxicircle architecture and evolutionary insights into Trypanosoma cruzi complex
Authors: Berná Luisa , Greif Gonzalo , Pita Sebastián , Faral-Tello Paula , Díaz-Viraqué Florencia , Souza Rita De Cássia Moreira De , Vallejo Gustavo Adolfo , Alvarez-Valin Fernando , Robello Carlos
Published: August 2021

We sequenced maxicircles fromT.cruzistrains representative of the species evolutionary diversity by using long-read sequencing, which allowed us to uncollapse their repetitive regions, finding that their real lengths range from 35 to 50 kb.T.cruzimaxicircles have a common architecture composed of four regions: coding region (CR), AT-rich region, short (SR) and long repeats (LR). Distribution of genes, both in order and in strand orientation are conserved, being the main differences the presence of deletions affecting genes coding for NADH dehydrogenase subunits, reinforcing biochemical findings that indicate that complex I is not functional inT.cruzi. Moreover, the presence of complete minicircles into maxicircles of some strains lead us to think about the origin of minicircles. Finally, a careful phylogenetic analysis was conducted using coding regions of maxicircles from up to 29 strains, and 1108 single copy nuclear genes from all of the DTUs, clearly establishing that taxonomicallyT.cruziis a complex of species composed by group 1 that contains clades A (TcI), B (TcIII) and D (TcIV), and group 2 (1 and 2 do not coincide with groups I and II described decades ago) containing clade C (TcII), being all hybrid strains of the BC type. Three variants of maxicircles exist inT.cruzi: a, b and c, in correspondence with clades A, B, and C from mitochondrial phylogenies. While A and C carry maxicircles a and c respectively, both clades B and D carry b maxicircle variant; hybrid strains also carry the b- variant. We then propose a new nomenclature that is self-descriptive and makes use of both the phylogenetic relationships and the maxicircle variants present inT.cruzi.