bluuebunny/crossref_metadata_2025 huggingface dataset:
Characterization of SARS-CoV-2 and host entry factors distribution in a COVID-19 autopsy series
Authors: Wang Xiao-Ming , Mannan Rahul , Xiao Lanbo , Abdulfatah Eman , Qiao Yuanyuan , Farver Carol , Myers Jeffrey L. , Zelenka-Wang Sylvia , McMurry Lisa , Su Fengyun , Wang Rui , Pantanowitz Liron , Jentzen Jeffrey , Wilson Allecia , Zhang Yuping , Cao Xuhong , Chinnaiyan Arul M. , Mehra Rohit
Published: August 2021

Background

SARS-CoV-2 is a highly contagious virus that causes the disease COVID-19. We have recently reported that androgens regulate the expression of SARS-CoV-2 host entry factors ACE2 and TMPRSS2, and androgen receptor (AR) in lung epithelial cells. We also demonstrated that the transcriptional repression of the AR enhanceosome inhibited SARS-CoV-2 infection in vitro.

Methods

To better understand the various sites of SARS-CoV-2 infection, and presence of host entry factors, we extensively characterized the tissue distribution and localization of SARS-CoV-2 virus, viral replication, and host entry factors in various anatomical sites sampled via autopsy. We applied RNA in-situ-hybridization (RNA-ISH), immunohistochemistry (IHC) and quantitative reverse transcription polymerase chain reaction (qRT-PCR) approaches. We also assessed histopathological changes in SARS-CoV-2 infected tissues.

Results

We detect SARS-CoV-2 virus and viral replication in pulmonary tissues by RNA-ISH and IHC and a variety of non-pulmonary tissues including kidney, heart, liver, spleen, thyroid, lymph node, prostate, uterus, and colon by qRT-PCR. We observe heterogeneity in viral load and viral cytopathic effects among various organ systems, between individuals and within the same patient. In a patient with a history of kidney transplant and under immunosuppressant therapy, we observe an unusually high viral load in lung tissue by RNA-ISH, IHC and qRT-PCR. SARS-CoV-2 virus is also detected in this patent’s kidney, liver and uterus. We find ACE2, TMPRSS2 and AR expression to overlap with the infection sites.

Conclusions

This study portrays the impact of dispersed SARS-CoV-2 infection in diverse organ systems, thereby facilitating avenues for systematic therapeutic approaches.
Human health risk assessment of atmospheric mercury inhalation around three artisanal small-scale gold mining areas in Indonesia
Authors: Nakazawa Koyomi , Nagafuchi Osamu , Kawakami Tomonori , Inoue Takanobu , Elvince Rosana , Kanefuji Koji , Nur Isrun , Napitupulu Mery , Basir-Cyio Muhammad , Kinoshita Hazumu , Shinozuka Ken'ichi
Published: August 2021

To clarify the human health risk of inhalation of gaseous elemental mercury (GEM), we measured GEM concentrations in three artisanal small-scale gold mining (ASGM) areas of Palu (Central Sulawesi), Muara Aman (Benkulu in Sumatra), and Palangka Raya (Central Kalimantan).
Ultrasensitive quantification of extracellular vesicles through dual signal amplification for the early diagnosis and prognosis of chronic obstructive pulmonary disease (COPD)
Authors: Xie Jingjun , Wu Can
Published: August 2021

Accurate quantification of low-abundant EVs plays an essential role in the diagnosis and treatment of chronic obstructive pulmonary disease (COPD).
Transdermal delivery of multifunctional CaO2@Mn-PDA nanoformulations by microneedles for NIR-induced synergistic therapy against skin melanoma
Authors: Ruan Liming , Song Gao , Zhang Xueya , Liu Tianqi , Sun Yanfang , Zhu Junlan , Zeng Zhiyong , Jiang Guohua
Published: August 2021

The CaO2@Mn-PDA nanoformulations, integrated with photothermal conversion of Mn-PDA, CDT of doped Mn ions, and relieve hypoxia in TME of CaO2, were developed for NIR-induced synergistic therapy against melanoma by microneedles transdermal delivery.
Low-temperature Fe–MnO2 nanotube catalysts for the selective catalytic reduction of NOx with NH3
Authors: Fan Hao , Fan Jie , Chang Tian , Wang Xiuru , Wang Xin , Huang Yu , Zhang Yang , Shen Zhenxing
Published: August 2021

Fe improved the reducibility of Mn sites and reduced the oxidizing properties of bridging oxygen.
Molecular characterization of ultrafine particles using extractive electrospray time-of-flight mass spectrometry
Authors: Surdu Mihnea , Pospisilova Veronika , Xiao Mao , Wang Mingyi , Mentler Bernhard , Simon Mario , Stolzenburg Dominik , Hoyle Christopher R. , Bell David M. , Lee Chuan Ping , Lamkaddam Houssni , Lopez-Hilfiker Felipe , Ahonen Lauri R. , Amorim Antonio , Baccarini Andrea , Chen Dexian , Dada Lubna , Duplissy Jonathan , Finkenzeller Henning , He Xu-Cheng , Hofbauer Victoria , Kim Changhyuk , Kürten Andreas , Kvashnin Aleksandr , Lehtipalo Katrianne , Makhmutov Vladimir , Molteni Ugo , Nie Wei , Onnela Antti , Petäjä Tuukka , Quéléver Lauriane L. J. , Tauber Christian , Tomé António , Wagner Robert , Yan Chao , Prevot Andre S. H. , Dommen Josef , Donahue Neil M. , Hansel Armin , Curtius Joachim , Winkler Paul M. , Kulmala Markku , Volkamer Rainer , Flagan Richard C. , Kirkby Jasper , Worsnop Douglas R. , Slowik Jay G. , Wang Dongyu S. , Baltensperger Urs , Haddad Imad el
Published: August 2021

Using real-time simultaneous gas- and particle-phase data, the condensation of naphthalene and β-caryophyllene oxidation products on a molecular level is discussed.
Synthesis and antitumour evaluation of indole-2-carboxamides against paediatric brain cancer cells
Authors: Alsayed Shahinda S. R. , Suri Amreena , Bailey Anders W. , Lane Samuel , Werry Eryn L. , Huang Chiang-Ching , Yu Li-Fang , Kassiou Michael , Sredni Simone Treiger , Gunosewoyo Hendra
Published: August 2021

Indole-2-carboxamides: antitumour potential and selectivity against paediatric glioma.
Photocatalytic performance, anti-bacterial activities and 3-chlorophenol sensor fabrication using MnAl2O4·ZnAl2O4 nanomaterials
Authors: Subhan Md Abdus , Chandra Saha Pallab , Hossain Anwar , Asiri Abdullah M. , Alam M. M. , Al-Mamun Mohammad , Ghann William , Uddin Jamal , Raihan Topu , Azad A. K. , Rahman Mohammed M.
Published: August 2021

The proposed mechanism for the determination of 3-CP by MnAl2O4·ZnAl2O4 nanomaterial/Nafion/GCE.
A carbon-based material with a hierarchical structure and intrinsic heteroatom sites for sodium-ion storage with ultrahigh rate and capacity
Authors: Cui Xue-Yang , Lin Xiao-Dong , Wang Ya-Jing , Xu Pan , Fan Xiao-Xiang , Zheng Ming-Sen , Chen Jia-Jia , Dong Quan-Feng
Published: August 2021

A hierarchically structured and intrinsically-heteroatom-containing carbon-based material is constructed and employed as both cathode and anode for sodium-ion capacitors, achieving both high energy density and power density.
Coupling of ReS2 nanosheet arrays with hollow NiCoS4 nanocubes enables ultrafast Na+ diffusion kinetics and super Na+ storage of a NiCoS4@ReS2 heterostructure
Authors: Li Zhiyong , Sun Rui , Qin Zhaoxia , Liu Xinlong , Wang Caihong , Lu Shengjun , Zhang Yufei , Fan Haosen
Published: August 2021

In this paper, NiCoS4@ReS2 heterostructure has been successfully constructed by anchoring ReS2 nanosheet arrays on hollow NiCoS4 nanocubes, which demonstrated outstanding rate capability and ultra-stable cycling performance for SIBs.
Asymmetric total synthesis and antidepressant activity of (−)-sila-mesembranol bearing a silicon stereocenter
Authors: Luo Gan , Chen Lingmin , Li Yi , Fan Yu , Wang Duyang , Yang Yufan , Gao Lu , Jiang Ruotian , Song Zhenlei
Published: August 2021

Asymmetric total synthesis of (−)-sila-mesembranol, the silicon analog of the natural alkaloid (−)-mesembranol has been achieved in 3.3% yield over 11 steps. The synthetic (−)-sila-mesembranol in mice exhibits better antidepressant effects than its carbon counterpart.
Site-specific role of bifunctional graphitic carbon nitride catalyst for the sustainable synthesis of 3,3-spirocyclic oxindoles in aqueous media
Authors: Dandia Anshu , Mahawar Dinesh Kumar , Saini Pratibha , Saini Surendra , Gupta Shyam L. , Rathore Kuldeep S. , Parewa Vijay
Published: August 2021

Functionalized graphitic carbon nitride (Sg-C3N4) has been manufactured and used as a reusable catalyst for the one-pot production of various spiro-pyrano chromenes and spiro indole-3,1′-naphthalene tetracyclic systems in aqueous media.
Antibacterial and antibiofilm activities of silver-decorated zinc ferrite nanoparticles synthesized by a gamma irradiation-coupled sol–gel method against some pathogenic bacteria from medical operating room surfaces
Authors: Abdel Maksoud M. I. A. , El-Sayyad Gharieb S. , El-Bastawisy Hanan S. , Fathy Rasha M.
Published: August 2021

This work aimed at the gamma irradiation-assisted synthesis of silver (Ag)-decorated ZnFe2O4(ZFO) ferrite nanoparticles (NPs), which were tested for their antibacterial and antibiofilm activities against some pathogenic bacteria from medical operating room surfaces.
Mesoporous MnFe2O4 magnetic nanoparticles as a peroxidase mimic for the colorimetric detection of urine glucose
Authors: Liu Ke , Su Jiaxing , Liang Jiangong , Wu Yuan
Published: August 2021

Schematic illustration of glucose detection with glucose oxidase (GOx) and mMnFe2O4 MNPs-catalyzed system.
Computational insights into structural, electronic, and optical properties of Janus GeSO monolayer
Authors: Do Thi-Nga , Hieu Nguyen N. , Poklonski N. A. , Thanh Binh Nguyen Thi , Nguyen Cuong Q. , Hien Nguyen D.
Published: August 2021

Although O is an element of chalcogen group, the study of two-dimensional (2D) O-based Janus dichalcogenides/monochalcogenides, especially their 1T-phase, has not been given sufficient attention.
Multi PCET in symmetrically substituted benzimidazoles
Authors: Odella Emmanuel , Secor Maxim , Elliott Mackenna , Groy Thomas L. , Moore Thomas A. , Hammes-Schiffer Sharon , Moore Ana L.
Published: August 2021

Proton-coupled electron transfer (PCET) reactions depend on the hydrogen-bond connectivity between sites of proton donors and acceptors.
Rigid two-dimensional indium metal–organic frameworks boosting nitrogen electroreduction at all pH values
Authors: Sun Yuntong , Xia Baokai , Ding Shan , Yu Licheng , Chen Sheng , Duan Jingjing
Published: August 2021

Rigid 2D In-MOF nanosheets is investigated as electrocatalysts for nitrogen electroreduction in the entire pH range for the first time, which follows an enzymatic mechanism, with the potential determining step being *H2NNH2* → *NH2 + NH3.
Redox-copolymers for the recovery of rare earth elements by electrochemically regenerated ion-exchange
Authors: Vapnik Haley , Elbert Johannes , Su Xiao
Published: August 2021

A unique copolymer combines ion-exchange groups and redox-active ferrocene groups to enable effective adsorption of rare earth element ions and fully electrochemically-controlled regeneration, without the use of hazardous chemicals.
Riveting the atomically distributed lithiophilic centers in the CNT-reinforced interfacial layer: an ultrathin, light-weight deposition substrate toward superior Li utilization
Authors: Zhao Ting , Li Shaowen , Wang Yanzhi , Wang Helin , Zhang Min , Tang Xiaoyu , Liu Fu , Du Dou , Zheng Haoquan , Ma Yue
Published: August 2021

Superior Li utilization is realized via an ultrathin, lightweight interfacial layer with atomically riveted lithiophilic Zn and interweaved carbon nanotubes.
Stable alkali metal anodes enabled by crystallographic optimization – a review
Authors: Bao Weizhai , Wang Ronghao , Li Bingqin , Qian Chengfei , Zhang Zherui , Li Jingfa , Liu Fangyang
Published: August 2021

Schematic illustration of the relationship between dendrite-free nucleation behavior and crystallographic optimization.
Long-life Na-rich nickel hexacyanoferrate capable of working under stringent conditions
Authors: Sun Yunpo , Xu Yunli , Xu Zheng , Sun Yu , Xu Xiongwen , Tu Jian , Xie Jian , Liu Shuangyu , Zhao Xinbing
Published: August 2021

Na-rich, large-size NiHCF exhibits an ultralong cycle life and excellent rate capacity, and is capable of working under stringent conditions.
Calcium carbonate particles: synthesis, temperature and time influence on the size, shape, phase, and their impact on cell hydroxyapatite formation
Authors: Sovova Sarka , Abalymov Anatolii , Pekar Miloslav , Skirtach Andre G. , Parakhonskiy Bogdan
Published: August 2021

To develop materials for drug delivery and tissue engineering and to study their efficiency with respect to ossification, it is necessary to apply physicochemical and biological analyses.
3D printing of biphasic inks: beyond single-scale architectural control
Authors: Cidonio Gianluca , Costantini Marco , Pierini Filippo , Scognamiglio Chiara , Agarwal Tarun , Barbetta Andrea
Published: August 2021

To date, Additive Manufacturing (AM) has come to the fore as a major disruptive technology embodying two main research lines – developing increasingly sophisticated printing technologies and new processable materials.
Self-assembled dipoles of o-carborane on gate oxide tuning charge carriers in organic field effect transistors
Authors: Chu Ming , Zhang Jie , Zeng Xingwei , Chen Zefeng , Liu Danqing , Chen Han , Xie Zuowei , Xu Jianbin , Miao Qian
Published: August 2021

A novel self-assembled monolayer of o-carborane on gate oxide not only realized p-channel organic field effect transistors with low threshold voltage and high field effect mobility, but also enabled ambipolar charge transport in a typical n-type organic semiconductor.
Fabrication of complex hierarchical heterostructures with controlled luminescence via seeded self-assembly
Authors: Liu Yin , Chang Lulu , Zhang Weiwei , Liu Shuya , Gong Yanjun
Published: August 2021

A complex hierarchical heterostructure transformed from laterally grown nanofibers to nanosheets and 3D microblocks can be fabricated via seeded self-assembly of molecules 1–3. The formation of heterostructure with blue and yellow emissions was achieved via co-assembled seeds method.
Semitransparent polymer solar cells floating on water: selected transmission windows and active control of algal growth
Authors: Yin Luqi , Zhou Yao , Jiang Tong , Xu Yunxiang , Liu Tong , Li Na , Zhou Ke , Yu Liangmin , Guo Cui , Murto Petri , Xu Xiaofeng
Published: August 2021

High-performance semitransparent polymer solar cells were demonstrated for synergistic control of solar energy generation on water bodies and algal growth in diverse aquatic habitats.
Transient mixed lubrication model of the human knee implant
Authors: Butt Hamza , Nissim Lee , Gao Leiming , Myant Connor , de Boer Greg , Hewson Robert
Published: August 2021

The human knee implant is computationally modelled in the mixed lubrication regime to investigate the tribological performance of the implant. This model includes the complex geometry of the implant components, unlike elliptical contact models that approximate this geometry. Film thickness and pressure results are presented for an ISO gait cycle to determine the lubrication regime present within the implant during its operation. It was found that it was possible for the lubrication regime to span between elastohydrodynamic, mixed and boundary lubrication depending on the operating conditions of the implant. It was observed that the tribological conditions present in one condyle were not necessarily representative of the other. Multiple points of contact were found within the same condyle, which cannot be computed by the elliptical contact solvers. This model can be used to balance forces in all directions, instead of only the normal loads, as often done in elliptical contact models. This work is an initial step towards understanding the role of the complex geometry in the tribological characteristics of the human knee implant when operating in physiological conditions.
Adaptive second‐order terminal PID sliding mode control design for integer‐order approximation of wind turbine system for maximum power extraction
Authors: Abolvafaei Mahnaz , Ganjefar Soheil
Published: August 2021

The main purpose of this paper is to extract the maximum power from the variable speed wind turbine (VSWT), which is modelled using fractional calculus. The use of the fractional‐order operator can harden the practical implementation and numerical simulation of the fractional‐order systems. To apply the fractional calculus theory, we assume that the orders of all fractional derivatives of the system have a small deviation from the nearest integers. By defining this small deviation as a perturbation parameter, an integer‐order approximation method is presented for approximating the fractional‐order system into a perturbed integer‐order system in the time domain. Then, a new adaptive second‐order sliding mode control (SOSMC) method is proposed using the terminal proportional integral derivative (TPID) sliding surface to achieve maximum power extraction and reduce mechanical loads and chattering. A TPID sliding surface is employed to ensure better tracking, have a zero steady‐state error, decrease the mechanical stresses, and eliminate the chattering phenomenon. The stability of the adaptive SOSMC based on the obtained integer‐order approximation is analyzed using the Lyapunov stability criterion. The simulation results of the proposed method are presented and compared with some designed controllers for wind turbines (WTs) modelled with fractional and integer derivatives. The obtained results show the effectiveness of the proposed strategy.
Ex-situ exploration of cemani chicken in Balai Penelitian Ternak (Balitnak), Bogor-West Java
Authors: Kostaman Tatan , Sopiyana Soni , Isbandi  , Pasaribu Tiurma
Published: August 2021

Cemani chicken is the rarest chicken in the world and generally in Indonesia is associated with medication and ritual ceremonies. The purpose of the research to determine the performance of cemani chickens that are kept outside their habitat. A total of 20 hens kept in litter cages was observed in the exploration. The hens were given commercial feed and drinking water was given ad libitum. The observed variable were hen day production (%), first egg weight (g), egg quality, and growth (g). All data obtained were analyzed descriptively. The results showed that hen day production (%) during 6 months of production increased, from 14.96% at the beginning of production to 48.97%. The first egg weight was 31.31 ± 1.43 g with the egg quality is almost the same as the quality of other local/native chicken eggs. The average body weight of DOC was 25.13 g/head, 8 weeks 839.94 g/head (♂) and 759.98 g/head (♀), and 20 weeks 1537.29 g/head (♂) and 1455.18 g/head (♀). The observed from the data obtained, the performance of cemani chicken in Balitnak showed hen day production, first egg weight, and DOC weight was slightly lower, but for 20-weeks bodyweight, growth was relatively higher.
The Effect of Colistin Administration as Medicated Feed on Alanine Aminotransferase and Creatinine Level in Broiler Infected with Escherichia coli
Authors: Nurul Fitri Aisah , Fitriana Ida , Windraningtyas Rosetyadewi Antasiswa , Muhtar Pratama Anggi , Ika Septiana Aria , Cahyo Budi Setiawan Dwi , Dwi Wijayanti Agustina
Published: August 2021

Colistin is a decapeptide antibiotic with narrow spectrum activity, mainly used as treatment for Gram negative bacteria. This study aims to scientifically determine the effect of colistin administration as medicated feed on alanine aminotransferase (ALT) and creatinine level in broiler infected with Escherichia coli. KTOP group as positive control, KTON group as negative control, while I, II, and III groups were infected with Escherichia coli 1 x 108 CFU/ml 0.1 ml via intratracheal route. Group I, II, and III were given colistin treatment dosage of 0.3 g/kg food, 0.6 g/kg food, and 1.2 g/kg food. Blood samples were taken through brachial veins for ALT and creatinine examination with a Caretium NB-201 semi-auto chemistry analyzer. Data were examined statistically using IBM SPSS Statistics 24 software and graphically using Microsoft Excel 365. Conclusion of the research by statistical analysis with Kruskal-Wallis test obtained ALT test results P = 0.147 and creatinine test results P = 0.815. Based on the results of this study, the administration of colistin medicated feed did not cause a significant effect on ALT and creatinine level in broiler infected with Escherichia coli, indicating that colistin has low potential toxicity while given as medicated feed.
Potential of goat manure as organic fertilizer in North Sumatera
Authors: Batubara Siti Fatimah , Santoso Agung Budi , El Ramija Khadijah
Published: August 2021

The North Sumatera province has the fifth largest goat population in Indonesia after Central, East, Lampung and West Java. Meanwhile, solid and liquid goat manures have great potential as a source of organic fertilizer. Therefore, this study aims to examine the potential of goat manure as a source of organic fertilizer and its role in improving soil quality, growth and crop production. The data were collected from the Central Bureau of Statistics and the results of previous studies. Furthermore, the potential of goat manure was calculated by multiplying the total goat population in North Sumatra by the goat manure production /head/day and converted to one year. The parameter measured was the total goat population in North Sumatera, goat manure production/head/day, and the covered agricultural land area. The results showed that goat manure only fulfilled 3.69% of the agricultural land area in North Sumatera. In addition, the case study in Deli Serdang District showed that the application of goat manure compost with biourine and balanced inorganic fertilizers increased red chilies’ productivity by 46%. Therefore, it was concluded that the potential of goat manure as organic fertilizer is still very low.
A review: the prevalence of dermatophytosis on cats in Indonesia and Turkey
Authors: Zaki Fatin Hanani Md , Airin Claude Mona , Nururrozi Alfarisa , Yanuartono  , Indarjulianto Soedarmanto
Published: August 2021

Dermatophytosis (ringworm) is an important feline skin disease primarily caused by the dermatophyte genera Microsporum and Trichophyton which may be affected by climate. Studying the prevalence of dermatophytosis on cats in Indonesia and Turkey was the main purpose of this article review. The articles reviewed were two articles from Turkey published consecutively on year 2011 and 2016, and an article from Indonesia published on year 2017. The findings showed that the prevalence of dermatophytosis in Indonesia was 17/30 (56.7%) while Turkey was 52/428 (12.1%). The age of the infected animals was the only predictor that had a major effect on the incidence of dermatophytosis on cats, as shown by the excellent positive cases of cats under one year of age relative to other age groups. In conclusion, the prevalence of dermatophytosis on cats in Turkey was slightly lower compared to the prevalence of feline dermatophytosis in subtropical country (Indonesia) and the variations may be attributed to the variation in humidity and temperature faced in both countries.
Re-epithelization and density of collagen fibers on wound healing of mice’s skin (Mus musculus) that treated with combination of chitosan membrane and eel (Monopterus albus) mucous
Authors: Djatumurti Deaoxi Renaschantika , Rafida Afifatur , Manalu Asha Yonika Putri , Pangestiningsih Tri Wahyu
Published: August 2021

Untreated skin wound can inhibit the wound healing process. Chitosan and eel mucous have biodegradable, biocompatible, and antimicrobial properties. This study aimed to determined the potential of combination between chitosan membrane and eel mucous extract in skin wound re-epithelization and collagen fibers deposition. Thirty adult male mice were divided into 5 groups, 6 animals/group. Skin wo und were perform by punch biopsy in 0.5 cm diameter. Group I-IV respectively recieved: 10% povidone iodine; eel mucus extract and gauze; combination of 1 % chitosan membrane and eel mucus; 1% chitosan membrane. Group V without therapy. Therapy was given once a day for 10 days. At the 5th and 10th half of animals/group were euthanized. Wound skin area were collected for hematoxylin-eosin and Mallory-azan stainings. Epithelial thickness and collagen density were observed and analyzed statistically. The result s showed significant difference in epithelial thickness on the 5th and 10th days (P ≤ 0.05) in combination group. Percentage of collagen density at 10th day of combination group showed significantly difference (P ≤ 0.05) compared with control. The conclusion is combination of 1 % chitosan membrane and eel mucous extract has the most potential to re-epithelization and increase density of collagen fibers in skin wound healing.
Effectiveness of Povidone Iodine and Antibiotic Treatment on Postpartum Reproductive Disorders in Beef Cattle
Authors: Setyawan Erif Maha Nugraha , Adi Yosua Kristian , Gustari Sri , Kusumawati Asmarani , Budiyanto Agung , Prihatno Surya Agus
Published: August 2021

This research was conducted to find out the reproductive disorders of postpartum and the effectiveness of its treatment in various nations of beef cattle. A total of 30 beef cattle raised in cattle groups in the D.I.Y. area was used as research samples. Cows are divided into three groups namely control group, iodine povidone infusion group, and antibiotic infusion group. First, second, and third months postpartum are performed clinical examination, blood collection, and rectovaginal examination. Haematological and clinical conditions in postpartum beef cattle have variations but most show a high profile of leukocytes in 1 st to 5th week. Povidone iodine infusion treatment in 1 st week postpartum can reduce bacterial infection until 5th week and can accelerate the uterine involution process during the recovery period.
The Effect of Common Detergents on The Causative Virus of Newcastle Disease
Authors: Nuradji Harimurti , Luthfiya Azmy Anistisha , Aquatica Ghea , Indi Dharmayanti NLP
Published: August 2021

Newcastle disease is one of the most severe poultry viral diseases due to its ability to cause massive economic losses and about 100% mortality in chickens. Many disinfectants have been used on farms to prevent the disease. However, the use of existing commercial disinfectants nowadays is considered expensive. The purpose of this research is to evaluate the effectiveness of commercial detergents as disinfectants in inactivating the virus. Two commercial detergents containing Alkylbenzene sulfonates, which can dissolve the viral envelope lipid, were tested. More so, three concentrations of 1%, 1.5%, and 2% were used, with contact times of 5, 10, and 15 minutes, respectively. The commercial disinfectant Virkon was employed as a control. The results showed that commercial detergents had the same results compared to control by being able to inactivate the virus with a concentration of 1%, 1.5%, and 2% in 5, 10, and 15 minutes, respectively. This shows that simple and inexpensive household detergents can be used as an alternative for disinfection.
Accessibilty analysis of tsunami evacuation route to self supported shelter in sub-district Pasie Nan Tigo, Padang City
Authors: Anas Ismail Febrin , Masrilayanti  , Yuli Anggraini Tria
Published: August 2021

The city of Padang, the capital of West Sumatra, has 1 million populations and located on the west coast of Sumatra. The city situated at two earthquake sources that are subduction zone in the Indian Ocean and Sumatra fault inland of Sumatra. Since the year 2006, Padang city is often experiencing an earthquake from both sources. In Mentawai island, about 200 km from Padang City westward, there is still what so-called seismic gap that very potential to generate big earthquake followed by a tsunami. To anticipate this, the mitigation measurements are needed to prepare the people on the west coast of Sumatra, especially in Padang city. One of the activities is to prepare the shelter that can cover around 600,000 people prone to tsunami near the beach. The infrastructures for shelter are very limited. There are only 4 shelters that have been built that have capacity about 2000-3000 people. To anticipate this condition, it needs to build what so-called self-supported shelter. The self-supported shelter is an idea or concept of utilizing a mosque or musholla to be a shelter by participating in the community surrounding its construction and management. The shelter will have a function as the ritual of religion and the tsunami evacuation place. Mosque or musholla is selected to shelter since it does not need to buy land, available in the near residence area, and easy to get funds in its construction. There are some aspects need to be prepared in order to function a shelter well, that is, the selection of location, the evacuation system, the construction method, the accessibility, and the structural design. This paper focus on analysis of the accessibility of evacuation routes to self-supported shelter in terms of time estimation, road facilities, and barrier during evacuation. The case study is chosen as the sub-district of Pasie Nan Tigo that has about 12,000 populations. The result can be a model in designing accessibility to self-supported shelters in the other area.
Seismic response of cable-stayed bridge subjected to single-support excitation on various soil condition
Authors: Masrilayanti  , Prayoga Nasution Ade , Kurniawan Ruddy
Published: August 2021

For cable-stayed bridge, pylon and girder are one of the most important factors in the design process. Because of the length this structure, it needs to consider the type of the soil because different soil type can be resulting a different earthquake loads. In this study, the behavior of superstructure was investigated using time history analysis subjected to excitation uniformly on the pylon and girder. The test model was a cable-stayed bridge which classified as a long-span bridge. For obtaining the effects of soil type condition, different response spectrums are considered for three soil types: firm, medium, and soft soil. The response spectrums were thus converted to become ground acceleration time history and displacement time history. The displacement was then applied longitudinally and transversally to the supports of the structure to determine the behavior of the bridge. The result shows that the maximum displacement on the pylon and girder due to longitudinal load was at the top of the pylon and in the middle of the main span. As for the transverse earthquake load, the maximum displacement was in the middle area of the pylon and the middle of the main span. The results also defines that the displacement caused by firm soil is smaller than medium soil and soft soil.
Evaluation of concretization of local road in Padang city using the importance satisfaction analysis and customer satisfaction index methods
Authors: Yosritzal  , Nofriyanti Elsa , Yossyafra
Published: August 2021

A road is the most critical infrastructure in economic development; therefore, it should be maintained at a certain level of service. In improving road quality, the satisfaction of road users can also be used as a reference to determine whether the road is still in good condition or if handling is needed to improve the comfort of the road users. This study aims to map the attributes that affect the satisfaction of local road users using the Importance Satisfaction Analysis and Customer Satisfaction Index methods, identify the main priority attributes that need to be improved, and assess the impact of concretization according to the community perceptions. The study found that road supporting facilities (road shoulder, drainage), the width of the road, smooth flow in and out of the road, prevention of stagnant water during the rainy season are the most priority attributes to be improved. The satisfaction index value is 67.22%, suggesting that overall, road users are satisfied with the existence of local road concretization in the city of Padang.
EsbRootView, a portable event display for the ESSnuSB project
Authors: Barrand Guy
Published: August 2021

EsbRootView is an event display for the detectors of ESSnuSB able to exploit natively all the nice devices that we have in hands today; desktop, laptops, but also smartphones and tablets.
Public Engagement in a Global Pandemic
Authors: Corbett Greg , Collier Ian , Palmer Sophy , Dack Tom , Liu Xin Ran
Published: August 2021

UKRI/STFC’s Scientific Computing Department (SCD) has a long and rich history of delivering face to face public engagement and outreach, both on site and in public places, as part of the wider STFC programme. Due to the global COVID-19 pandemic, SCD was forced to abandon an extensive planned programme of public engagement, alongside altering the day-to-day working methods of the majority of its staff. SCD had to respond rapidly to create a new, remote only, programme for the summer and for the foreseeable future. This was initially an exercise in improvisation, identifying existing activities that could be delivered remotely with minimal changes. As the pandemic went on, SCD also created new resources specifically for a remote audience and adapted existing activities where appropriate, using our evaluation framework to ensure these activities continued to meet the aims of the in-person programme. This paper presents the process through which this was achieved, some of the benefits and challenges of remote engagement and the plans for 2021 and beyond.
Systematic benchmarking of HTTPS third party copy on 100Gbps links using XRootD
Authors: Fajardo Edgar , Arora Aashay , Davila Diego , Gao Richard , Würthwein Frank , Bockelman Brian
Published: August 2021

The High Luminosity Large Hadron Collider provides a data challenge. The amount of data recorded from the experiments and transported to hundreds of sites will see a thirty fold increase in annual data volume. A systematic approach to contrast the performance of different Third Party Copy (TPC) transfer protocols arises. Two contenders, XRootD-HTTPS and the GridFTP are evaluated in their performance for transferring files from one server to another over 100Gbps interfaces. The benchmarking is done by scheduling pods on the Pacific Research Platform Kubernetes cluster to ensure reproducible and repeatable results. This opens a future pathway for network testing of any TPC transfer protocol.
Fine-grained data caching approaches to speedup a distributed RDataFrame analysis
Authors: Padulano Vincenzo Eduardo , Tejedor Saavedra Enric , Alonso-Jordá Pedro
Published: August 2021

Thanks to its RDataFrame interface, ROOT now supports the execution of the same physics analysis code both on a single machine and on a cluster of distributed resources. In the latter scenario, it is common to read the input ROOT datasets over the network from remote storage systems, which often increases the time it takes for physicists to obtain their results. Storing the remote files much closer to where the computations will run can bring latency and execution time down. Such a solution can be improved further by caching only the actual portion of the dataset that will be processed on each machine in the cluster, reusing it in subsequent executions on the same input data. This paper shows the benefits of applying different means of caching input data in a distributed ROOT RDataFrame analysis. Two such mechanisms will be applied to this kind of workflow with different configurations, namely caching on the same nodes that process data or caching on a separate server.
Enabling interoperable data and application services in a federated ScienceMesh
Authors: Arora Ishank , Alfageme Sainz Samuel , Ferreira Pedro , Gonzalez Labrador Hugo , Moscicki Jakub
Published: August 2021

In recent years, cloud sync & share storage services, provided by academic and research institutions, have become a daily workplace environment for many local user groups in the High Energy Physics (HEP) community. These, however, are primarily disconnected and deployed in isolation from one another, even though new technologies have been developed and integrated to further increase the value of data. The EU-funded CS3MESH4EOSC project is connecting locally and individually provided sync and share services, and scaling them up to the European level and beyond. It aims to deliver the ScienceMesh service, an interoperable platform to easily sync and share data across institutions and extend functionalities by connecting to other research services using streamlined sets of interoperable protocols, APIs and deployment methodologies. This supports multiple distributed application workflows: data science environments, collaborative editing and data transfer services.

In this paper, we present the architecture of ScienceMesh and the technical design of its reference implementation, a platform that allows organizations to join the federated service infrastructure easily and to access application services outof-the-box. We discuss the challenges faced during the process, which include diversity of sync & share platforms (Nextcloud, Owncloud, Seafile and others), absence of global user identities and user discovery, lack of interoperable protocols and APIs, and access control and protection of data endpoints. We present the rationale for the design decisions adopted to tackle these challenges and describe our deployment architecture based on Kubernetes, which enabled us to utilize monitoring and tracing functionalities. We conclude by reporting on the early user experience with ScienceMesh.
MetaCat - metadata catalog for data management systems
Authors: Igor Mandrichenko
Published: August 2021

Metadata management is one of three major areas of scientific data management along with replica management and workflow management. Metadata is the information describing the data stored in a data item, a file or an object. It includes the data item provenance, recording conditions, format and other attributes. MetaCat is a metadata management database designed and developed for High Energy Physics experiments. As a component of a data management system, it’s main objectives are to provide efficient metadata storage and management and fast data selection functionality. MetaCat is required to work on the scale of 100 million files (or objects) and beyond. The article will discuss the functionality of MetaCat and technological solutions used to implement the product.
Distributed training and scalability for the particle clustering method UCluster
Authors: Sunneborn Gudnadottir Olga , Gedon Daniel , Desmarais Colin , Bengtsson Bernander Karl , Sainudiin Raazesh , Gonzalez Suarez Rebeca
Published: August 2021

In recent years, machine-learning methods have become increasingly important for the experiments at the Large Hadron Collider (LHC). They are utilised in everything from trigger systems to reconstruction and data analysis. The recent UCluster method is a general model providing unsupervised clustering of particle physics data, that can be easily modified to provide solutions for a variety of different decision problems. In the current paper, we improve on the UCluster method by adding the option of training the model in a scalable and distributed fashion, and thereby extending its utility to learn from arbitrarily large data sets. UCluster combines a graph-based neural network called ABCnet with a clustering step, using a combined loss function in the training phase. The original code is publicly available in TensorFlow v1.14 and has previously been trained on a single GPU. It shows a clustering accuracy of 81% when applied to the problem of multi-class classification of simulated jet events. Our implementation adds the distributed training functionality by utilising the Horovod distributed training framework, which necessitated a migration of the code to TensorFlow v2. Together with using parquet files for splitting data up between different compute nodes, the distributed training makes the model scalable to any amount of input data, something that will be essential for use with real LHC data sets. We find that the model is well suited for distributed training, with the training time decreasing in direct relation to the number of GPU’s used. However, further improvements by a more exhaustive and possibly distributed hyper-parameter search is required in order to achieve the reported accuracy of the original UCluster method.
ESCAPE Data Lake
Authors: Di Maria Riccardo , Dona Rizart ,   on behalf of the ESCAPE project
Published: August 2021

The European-funded ESCAPE project (Horizon 2020) aims to address computing challenges in the context of the European Open Science Cloud. The project targets Particle Physics and Astronomy facilities and research infrastructures, focusing on the development of solutions to handle Exabyte-scale datasets. The science projects in ESCAPE are in different phases of evolution and count a variety of specific use cases and challenges to be addressed.

This contribution describes the shared-ecosystem architecture of services, the Data Lake, fulfilling the needs in terms of data organisation, management, and access of the ESCAPE community. The Pilot Data Lake consists of several storage services operated by the partner institutes and connected through reliable networks, and it adopts Rucio to orchestrate data management and organisation. The results of a 24-hour Full Dress Rehearsal are also presented, highlighting the achievements of the Data Lake model and of the ESCAPE sciences.
FTS3: Data Movement Service in containers deployed in OKD
Authors: Lobato Pardavila Lorena , Holzman Burt , Karavakis Edward , Bryant Lincoln , Timm Steven
Published: August 2021

The File Transfer Service (FTS3) is a data movement service developed at CERN which is used to distribute the majority of the Large Hadron Collider’s data across the Worldwide LHC Computing Grid (WLCG) infrastructure. At Fermilab, we have deployed FTS3 instances for Intensity Frontier experiments (e.g. DUNE) to transfer data in America and Europe, using a container-based strategy. In this article we summarize our experience building docker images based on work from the SLATE project (slateci.io) and deployed in OKD, the community distribution of Red Hat OpenShift. Additionally, we discuss our method of certificate management and maintenance utilizing Kubernetes CronJobs. Finally, we also report on the configuration currently running at Fermilab.
Finalizing Construction of a New Data Center at BNL
Authors: Latif Imran , Misawa Shigeki , Zaytsev Alexandr
Published: August 2021

Computational science, data management and analysis have been key factors in the success of Brookhaven National Laboratory’s scientific programs at the Relativistic Heavy Ion Collider (RHIC), the National Synchrotron Light Source II (NSLS-II), the Center for Functional Nanomaterials (CFN), and in biological, atmospheric, and energy systems science, Lattice Quantum Chromodynamics (LQCD) and Materials Science, as well as our participation in international research collaborations, such as the ATLAS experiment at Europe’s Large Hadron Collider (LHC) at CERN (Switzerland) and the Belle II experiment at KEK (Japan). The construction of a new data center is an acknowledgement of the increasing demand for computing and storage services at BNL in the near term and enable the Lab to address the needs of the future experiments at the High-Luminosity LHC at CERN and the Electron-Ion Collider (EIC) at BNL in the long term.
Distributed statistical inference with pyhf enabled through funcX
Authors: Feickert Matthew , Heinrich Lukas , Stark Giordon , Galewsky Ben
Published: August 2021

In High Energy Physics facilities that provide High Performance Computing environments provide an opportunity to efficiently perform the statistical inference required for analysis of data from the Large Hadron Collider, but can pose problems with orchestration and efficient scheduling. The compute architectures at these facilities do not easily support the Python compute model, and the configuration scheduling of batch jobs for physics often requires expertise in multiple job scheduling services. The combination of the pure-Python libraries pyhf and funcX reduces the common problem in HEP analyses of performing statistical inference with binned models, that would traditionally take multiple hours and bespoke scheduling, to an on-demand (fitting) “function as a service” that can scalably execute across workers in just a few minutes, offering reduced time to insight and inference. We demonstrate execution of a scalable workflow using funcX to simultaneously fit 125 signal hypotheses from a published ATLAS search for new physics using pyhf with a wall time of under 3 minutes. We additionally show performance comparisons for other physics analyses with openly published probability models and argue for a blueprint of fitting as a service systems at HPC centers.
Decoding Photons: Physics in the Latent Space of a BIB-AE Generative Network
Authors: Buhmann Erik , Diefenbacher Sascha , Eren Engin , Gaede Frank , Kasieczka Gregor , Korol Anatolii , Krüger Katja
Published: August 2021

Given the increasing data collection capabilities and limited computing resources of future collider experiments, interest in using generative neural networks for the fast simulation of collider events is growing. In our previous study, the Bounded Information Bottleneck Autoencoder (BIB-AE) architecture for generating photon showers in a high-granularity calorimeter showed a high accuracy modeling of various global differential shower distributions. In this work, we investigate how the BIB-AE encodes this physics information in its latent space. Our understanding of this encoding allows us to propose methods to optimize the generation performance further, for example, by altering latent space sampling or by suggesting specific changes to hyperparameters. In particular, we improve the modeling of the shower shape along the particle incident axis.
Integration of JUNO simulation framework with Opticks: GPU accelerated optical propagation via NVIDIA® OptiX™
Authors: Blyth Simon
Published: August 2021

Opticks is an open source project that accelerates optical photon simulation by integrating NVIDIA GPU ray tracing, accessed via NVIDIA OptiX, with Geant4 toolkit based simulations. A single NVIDIA Turing architecture GPU has been measured to provide optical photon simulation speedup factors exceeding 1500 times single threaded Geant4 with a full JUNO analytic GPU geometry automatically translated from the Geant4 geometry. Optical physics processes of scattering, absorption, scintillator reemission and boundary processes are implemented within CUDA OptiX programs based on the Geant4 implementations. Wavelength-dependent material and surface properties as well as inverse cumulative distribution functions for reemission are interleaved into GPU textures providing fast interpolated property lookup or wavelength generation. In this work we describe major recent developments to facilitate integration of Opticks with the JUNO simulation framework including on GPU collection effciency hit culling which substantially reduces both the CPU memory needed for photon hits and copying overheads. Also progress with the migration of Opticks to the all new NVIDIA OptiX 7 API is described.
The use of Boosted Decision Trees for Energy Reconstruction in JUNO experiment
Authors: Gavrikov Arsenii , Ratnikov Fedor ,   on behalf of the JUNO Collaboration
Published: August 2021

The Jiangmen Underground Neutrino Observatory (JUNO) is a neutrino experiment with a broad physical program. The main goals of JUNO are the determination of the neutrino mass ordering and high precision investigation of neutrino oscillation properties. The precise reconstruction of the event energy is crucial for the success of the experiment.

JUNO is equiped with 17 612 + 25 600 PMT channels of two kind which provide both charge and hit time information. In this work we present a fast Boosted Decision Trees model using small set of aggregated features. The model predicts event energy deposition. We describe the motivation and the details of our feature engineering and feature selection procedures. We demonstrate that the proposed aggregated approach can achieve a reconstruction quality that is competitive with the quality of much more complex models like Convolution Neural Networks (ResNet, VGG and GNN).