bluuebunny/crossref_metadata_2025_split huggingface dataset:
Effects of different times of probiotic additions on floc abundance and growth of white leg shrimp (Litopenaeus vannamei): Laboratory scale cultivation
Authors: Samadan G M , Yuliana  , Masril R , Syazili A , Supyan  
Published: November 2021

AbstractWater quality management for aquaculture is very important because water is a living medium for aquaculture organisms. One of the technological products that use microbes to create a better environment by breaking down organic matter is probiotics. This study aims to determine the effects of different probiotic administration times on water quality in white leg shrimp culture at a laboratory scale. Juveniles of white leg shrimp with PL27 size were reared for 45 days and given four treatments with probiotics at different times. The result showed that the administration of probiotics with a short period interval had a significant effect on floc volume, absolute growth, survival rate, concentrations of ammonia, nitrate, and nitrite. Provision of probiotics with a short time span tended to reduce the concentration of ammonia, nitrate and nitrite. The difference in time of giving probiotics to bio-floc media increased the growth of white leg shrimp, improved water quality, and reduced the concentration of ammonia (NH3), nitrate (NO3), and nitrite (NO2).
The nursery of Litopenaeus vannamei at different density using aeration system on pond
Authors: Suwoyo H S , Sahrijanna A , Suwardi  , Pantjara B 
Published: November 2021

Abstract
The nursery of shrimp is an intermediate effort to connect hatchery and grow-out process, wherein shrimp fry was rear in a controlled process in a certain time before reared on pond. The study was aimed to evaluate the growth and, survival rate of white shrimp (L. vannamei) under different stocking density in nursery phase on pond. The nursery of L. vannamei was carried out at experimental pond installation of Research Institute for Coastal Aquaculture and Fisheries Extension (RICAFE) in Maros-South Sulawesi using a 5.5 x 11 m2 size of ponds, which was equipped with a bottom aeration system. The water depth of pond was 40 cm. Pond preparation was done by pond repairing, maintaining, drying, and eradicating using 20 ppm of saponin, flushing and water filling gradually until maximum of water level. The fry of L. vannamei (PL-10) with an average initial weight of 0.002g, which obtained from hatchery, were stocked. The treatments were stocking density of L. vannamei fry namely 1,653 individuals/m3 or 40,000 individuals/pond (A) and 909 individuals/m3 or 22,000 individuals/pond (B). Commercial powdered feed was given 3 times/day in 50–100% of biomass weight calculation base. The parameters observed were growth rate, survival rate of white shrimp and water quality condition. The results showed water quality variables including temperature, dissolved oxygen, pH, salinity, and alkalinity were in a suitable range for growth and survival of L. vannamei. The survival rate of L. vannamei in 21 days nursery was 86.40-95.61% and the final weight ranging from 0.292 to 0.320g/ind.
Role of Eleutherine bulbosa (Mill.) Urb. in shrimp and fish: a mini review
Authors: Munaeni W , Muchdar F , Aris M 
Published: November 2021

AbstractMedicinal plants have been commonly used in aquaculture to increase growth and immunity and control fish diseases as an effort to replace or as alternative to uses of chemical antibiotics and compounds. The use of medicinal plants in aquaculture provides safe and environmentally friendly compounds. Natural products of medicinal plants have been used in humans for thousands of years to treat disease. One of them isEleutherine bulbosa(Mill.) Urb. This article describes the potential ofE. bulbosaas an antibacterial, prebiotic, and antioxidant as well as its efficacy on aquatic organisms. Addition of extracts and powders ofE. bulbosathrough feed to white shrimpLitopenaeus vannameiwas able to improve growth performance, immune response, and resistance against infection from pathogenic bacteria. Optimal use ofE. bulbosaneeds to pay attention to dose and size of shrimp cultured. So far, administration ofE. bulbosapowder through feed was more effective and efficient than the use ofE. bulbosaextract in a large scale. Research onE. bulbosaas an immunostimulant in fish is still limited. Further research on the use ofE. bulbosashould be conducted to examine the effect ofE. bulbosaon growth performance and fish health on a large scale aquaculture.
The fishing season and the exploitation status of mud crab (Scylla serrata) in Asahan Sea, North Sumatera, Indonesia
Authors: Pane A R P , Kembaren D D , Mahiswara  , Suman A 
Published: November 2021

AbstractCrab is one of the resources that can be found in almost all areas in Indonesia, and its export increases every year. However, increase in its exploitation and mangrove forest damage affect crab availability.Scylla serratais one of the crab commodities for export in Asahan sea, North Sumatera. Scientific studies are necessary to determine the fishing season and the exploitation status of crabs in the area. Therefore, this study was carried out for 3 years, i.e. in April–December 2018, February–December 2019, and March–December 2020, at one crab landing site in Asahan. The fishing season forS. serratain this area occurred all year long, with peak seasons in April–June and September–December. The crab’s carapace width (CW) was 65–175 mm, where 71.2% of which were below 120 mm. Its carapace width at first capture (CWc) increased from 103.2 mm to 112.1 mm. Its fishing mortality (F) was 1.40 per year, higher than its natural mortality (M) (0.84 per year). Therefore, its exploitation rate (E) was 0.63, indicating that the species was already overfished. Suggested measures to control the fishing activity include limiting the crab size for capture in accordance with the Regulation of the Minister of Marine Affairs and Fisheries No. 12 Year 2020 and improving the environment of mangrove habitats.
Feeding ground indications are based on species, seagrass density and existence of Dugong dugon in Hiri Island Sea, North Maluku, Indonesia
Authors: Akbar N , Marus I , Ridwan R , Baksir A , Paembonan R E , Ramili Y , Tahir I , Ismail F , Wibowo E S , Inayah  , Madduppa H H , Subhan B , Wahab I , Hamsah H 
Published: November 2021

Abstract
Seagrass ecosystems are located between mangrove ecosystems and coral reefs. Seagrass ecosystems are habitats and foraging area for many marine organisms. Eco-biological cycles in seagrass ecosystems are important for maintaining populations of many organisms. Seagrass at Hiri Island is distributed horizontally along the coast. This island is also a location where Dugong dugon is found North Maluku. Dugong dugon is a vurneable species that has been included in the IUCN and Appendix I Cites. This study aimed to identify species, density of seagrass and existence of Dugong dugong. The survey method used quadratic transect method to collect seagrass data. The Results found 6 species of seagrass at Hiri Island. Five species of those seagrass (Cymodocea serrulata, Cymodecea rotundata, Halodule uninervis, Halodule pinifolia, Halophila spinulosa) are known as food of Dugong dugon. The highest species density was shown by Halodule uninervis. The presence of Dugong dugon and its feeding trail was found during field survey. Information on seagrass species and Dugong dugon sightings location can be used for endangered species conservation policies. Management and conservation efforts need to be done to maintain seagrass ecosystem and Dugong dugon potential habitat at Hiri Island.
Social-ecological system in Depapre Bay Area of Jayapura Papua Indonesia
Authors: Paulangan Y P , Barapadang B , Amin M A Al. , Tangkelayuk H 
Published: November 2021

Abstract
A Socio-Ecological Systems (SESs) are systems that connect human systems and natural systems by emphasizing that humans must be seen as part of, and cannot be separated from nature. Understanding SESs is very important as the main capital in planning the management of coastal and marine resources. The purpose of this study was to study SESs in Depapre Bay, Jayapura, Papua Province using the Drivers-Pressure-Impact-State-Responses (DPSIR) approach. Based on the research results, it was found that the issues and problems of SESs in Depapre Bay were related to the utilization of coastal and marine resources that were not environmentally friendly, such as the use of blast fishing and tuba root poisoning and development that did not consider the sustainability of coastal and marine resources. In addition, the response of the government and stakeholders has not focused on overcoming the damage to ecosystems and coastal and marine biological resources in an integrated manner. This can be seen from the programs carried out that are still partial, especially in the prevention of destructive fishing and the rehabilitation of coastal and marine ecosystems that have been damaged.
Dynamics of peat accumulation processes in the areas of the periglacial zone of the basin watershed of Tugur-Nimelen rivers
Authors: Chakov V V , Parkhomchuk E V , Zakharchenko E N 
Published: November 2021

Abstract
The paper considers the features of waterlogging of a flat watershed, unique in its structure and evolution, between the valley complexes of the two largest watercourses of Khabarovsk Territory. The Tugur and Nimelen rivers had rather powerful debit of water flows during the Pleistocene and were repeatedly redirected from the northern azimuth (the Sea of Okhotsk) to the southern one (the Amur catchment). This process continued partly at the early stages of the Holocene, as the stratigraphy of the peat deposits of the bogs formed indicates here.
Study on the Green Development Potential and International Cooperation Countermeasures of Primorsky Krai of Russia
Authors: Li F , Ji M , Cheng H , Dong S , Liu Q , Boldanov T 
Published: November 2021

Abstract
Green development and international cooperation are important themes of today’s social development research. As Russia’s important area to the Asia-Pacific region, the Primorsky Krai bears the responsibility of exploring international cooperation and green development methods. Based on the current situation of Russia’s development, this study constructs an evaluation index system for green development capabilities from the four aspects. Based on the entropy method, the 2015 first-level administrative unit of the Russian Federation was evaluated for green development capabilities, focusing on the status quo of the green development capabilities of the Primorsky Territory and the development direction of international cooperation. The results show that the Primorsky Krai has a relatively high level of green development capability in the Russian Federation. The price level of the Primorsky Territory has the strongest impact on the green development capability, and the industrial green development capability urgently needs to be improved. According to the evaluation results, it put forward suggestions that the Primorsky Krai needs to improve the development of green international cooperation in terms of social development, etc., and provided theoretical support.
Creation and research of new bioindifferent photocatalysts that use the energy of solar radiation to purify wastewater from pollutants
Authors: Makarevich K S , Kaminsky O I , Zaitsev A V , Kirichenko E A , Krutikova V O 
Published: November 2021

Abstract
This work is devoted to the study of new bioindifferent photocatalysts that use the energy of solar radiation to purify water from organic pollutants. Photocatalytic materials were obtained by a previously developed low-temperature pyrolytic synthesis. Varying the bismuth content in the percursor mixture within 15-30 %, allows controlling the phase formation of the bismuth and strontium silicate phases. The samples obtained at 25 % bismuth in the precursor mixture (in terms of Bi2O3 %, wt.) show the highest photocatalytic activity with Bi12SiO2, Bi4Si3O12 formed in the catalyst composition. Photocatalytic activity of coatings with the predominance of bismuth silicates is inferior to coatings with the predominance of strontium bismuthates, but their greater hydrolytic stability is observed.
Mapping the pyrogenic dynamics of forest geosystems on the northeastern shore of Lake Baikal
Authors: Myadzelets A V 
Published: November 2021

Abstract
The paper considers the impact of the pyrogenic factor on the landscapes of the Barguzinskii Range. Model representative sites with natural and disturbed mountain-taiga geosystems are identified in the territory of the Trans-Baikal National Park (Svyatoi Nos Peninsula) and the Barguzinskii Nature Reserve (Shumilikha, Tarkulik, and Davsha river valleys). We used geoinformation methods, landscape interpretation mapping, field observation data, remote sensing data and traditional comparative geographical methods for assessment and mapping. The collected data are systematized in the form of a geoinformation database for individual sections and visualized in a cartographic form. We compiled vegetation maps, taking into account the features of the relief and soil types and gave a general description of the landscape state to analyze the pyrogenic impact on local landscapes. It was also revealed that the modification processes of forest geosystems caused by the pyrogenic impact are widespread across wide swathes, but have a different character. It depends on the individual spatial geographical features of the selected representative sites and the nature and time of the direct pyrogenic factor exposure, e.g., the frequency, intensity, especially the microclimate, relief, etc. The paper shows that the restorative stages of plant dynamics in the model sites are clearly traced. We have established an insignificant difference between the current and reference states in places of weak pyrogenic impact, significant local state changes in places of extensive areal impact, and significant and catastrophic changes in places of lasting and intense pyrogenic impact. Maps of the geosystem disturbance caused by both pyrogenic and natural factors for the model sites were compiled.
Challenges and opportunities in network-based solutions for biological questions
Authors: Guo Margaret G , Sosa Daniel N , Altman Russ B 
Published: November 2021

Abstract
Network biology is useful for modeling complex biological phenomena; it has attracted attention with the advent of novel graph-based machine learning methods. However, biological applications of network methods often suffer from inadequate follow-up. In this perspective, we discuss obstacles for contemporary network approaches—particularly focusing on challenges representing biological concepts, applying machine learning methods, and interpreting and validating computational findings about biology—in an effort to catalyze actionable biological discovery.
CSM-carbohydrate: protein-carbohydrate binding affinity prediction and docking scoring function
Authors: Nguyen Thanh Binh , Pires Douglas E V , Ascher David B 
Published: November 2021

AbstractProtein-carbohydrate interactions are crucial for many cellular processes but can be challenging to biologically characterise. To improve our understanding and ability to model these molecular interactions, we used a carefully curated set of 370 protein-carbohydrate complexes with experimental structural and biophysical data in order to train and validate a new tool, cutoff scanning matrix (CSM)-carbohydrate, using machine learning algorithms to accurately predict their binding affinity and rank docking poses as a scoring function. Information on both protein and carbohydrate complementarity, in terms of shape and chemistry, was captured using graph-based structural signatures. Across both training and independent test sets, we achieved comparable Pearson’s correlations of 0.72 under cross-validation [root mean square error (RMSE) of 1.58 Kcal/mol] and 0.67 on the independent test (RMSE of 1.72 Kcal/mol), providing confidence in the generalisability and robustness of the final model. Similar performance was obtained across mono-, di- and oligosaccharides, further highlighting the applicability of this approach to the study of larger complexes. We show CSM-carbohydrate significantly outperformed previous approaches and have implemented our method and make all data freely available through both a user-friendly web interface and application programming interface, to facilitate programmatic access at http://biosig.unimelb.edu.au/csm_carbohydrate/. We believe CSM-carbohydrate will be an invaluable tool for helping assess docking poses and the effects of mutations on protein-carbohydrate affinity, unravelling important aspects that drive binding recognition.
Gastroesophageal reflux disease and salivary pepsin in patients with heterotopic gastric mucosa in the upper esophagus
Authors: Xiong Xin , He Suyu , Xu Fei , Xu Zhihong , Zhang Xiumei , Wang Hanmei , Liu Tianyu , Jia Yingdong 
Published: November 2021

Summary

Background
Heterotopic gastric mucosa in the upper esophagus (HGMUE) is reported to be related to gastroesophageal reflux disease (GERD). This study investigated the prevalence of GERD and the use of salivary pepsin to diagnose gastroesophageal reflux, especially proximal reflux, in HGMUE patients.

Methods
One hundred and fifty-three HGMUE patients and 50 healthy volunteers were studied. All subjects took a reflux symptom index questionnaire (RSI); underwent endoscopy, barium esophagogram, high-resolution manometry (HRM), and 24-hour multichannel intraluminal impedance-pH-metry (MII-pH); and salivary pepsin test.

Results
Ninety-five (62.1%) HGMUE patients but no control subjects were diagnosed with GERD. The salivary pepsin concentration, RSI score, DeMeester score, acid exposure time (AET), total reflux episodes, proximal acidic reflux episodes, and proximal weakly acidic reflux episodes were significantly higher in the HGMUE group than in the control group (P &lt; 0.05). The salivary pepsin test showed a sensitivity of 85.9% and specificity of 56.9% for diagnosing GERD using the optimal cut-off value of 75 ng/mL. One hundred and seven (69.9%) and 46 (30.1%) HGMUE patients were categorized as pepsin (+) and pepsin (−), respectively when 75 ng/mL was used as a cut-off value. Male sex, RSI, AET, and proximal acid reflux episodes were positive predictive factors for the occurrence of pepsin (+) in HGMUE patients.

Conclusions
GERD, especially GERD with proximal acid reflux and related symptoms, was common in HGMUE patients. The salivary pepsin test could be an additional useful test for testing reflux in HGMUE patients, but it will not replace the MII-pH.
Clinical, Endoscopic, and Safety Placebo Rates in Induction and Maintenance Trials of Crohn’s Disease: Meta-Analysis of Randomised Controlled Trials
Authors: Almradi Ahmed , Sedano Rocio , Hogan Malcolm , Zou G Y , MacDonald John K , Parker Claire E , Hanzel Jurij , Crowley Eileen , Singh Siddharth , D’Haens Geert , Sandborn William J , Feagan Brian G , Ma Christopher , Jairath Vipul 
Published: November 2021

Abstract

Background
Precision in estimating placebo rates is important for clinical trial design.

Aim
To quantify placebo rates across relevant endpoints in Crohn’s disease [CD] trials and identify the factors influencing these rates in a contemporary meta-analysis.

Methods
We searched MEDLINE, EMBASE, and CENTRAL from inception to March 2021. Eligible studies were placebo-controlled trials of pharmacological interventions for CD. Placebo response and remission rates for induction and maintenance trials were extracted and pooled by random-effects to quantify placebo rates across studies. Mixed-effects meta-regression was used to evaluate the effects of study-level characteristics on placebo rates.

Results
In 125 studies [91 induction, 46 maintenance], placebo clinical remission and response rates for induction studies were 18% (95% confidence interval [CI] 16, 21%], and 32% [95% CI 29, 35%], respectively, and for maintenance studies were 28% [95% CI 23, 34%] and 30% [95% CI 24, 37%], respectively. Endoscopic remission and response rates in induction studies were 8% [95% CI 4, 18%] and 16% [95% CI 11, 23%], respectively. Trials enrolling patients with prior biologic exposure, longer disease duration, and higher CD activity index scores were associated with lower placebo clinical remission rates. Increased duration of follow-up, more follow-up visits, and a greater proportion of patients with colonic disease distribution were associated with higher clinical placebo rates.

Conclusions
Placebo remission and response rates in CD trials vary according to the phase of the trial, endpoint assessed, and induction or maintenance design. These contemporary estimates will help to inform future CD trial design.
Barriers and facilitators to virtual education in cardiac rehabilitation: a systematic review of qualitative studies
Authors: Vanzella Lais Manata , Oh Paul , Pakosh Maureen , Ghisi Gabriela Lima de Melo 
Published: November 2021

Abstract

Background
Due to restrictions imposed by the severe acute respiratory syndrome coronavirus 2 pandemic much attention has been given to virtual education in cardiac rehabilitation (CR). Despite growing evidence that virtual education is effective in teaching patients how to better self-manage their conditions, there is very limited evidence on barriers and facilitators of CR patients in the virtual world.

Aims
To identify barriers and facilitators to virtual education participation and learning in CR.

Methods
A systematic review of peer-reviewed literature was conducted. Medline, Embase, Emcare, CINAHL, PubMed, and APA PsycInfo were searched from inception through April 2021. Following the PRISMA checklist, only qualitative studies were considered. Theoretical domains framework (TDF) was used to guide thematic analysis. The Critical Appraisal Skills Program was used to assess the quality of the studies.

Results
Out of 6662 initial citations, 12 qualitative studies were included (58% ‘high’ quality). A total of five major barriers and facilitators were identified under the determinants of TDF. The most common facilitator was accessibility, followed by empowerment, technology, and social support. Format of the delivered material was the most common barrier. Technology and social support also emerged as barriers.

Conclusion
This is the first systematic review, to our knowledge, to provide a synthesis of qualitative studies that identify barriers and facilitators to virtual education in CR. Cardiac rehabilitation patients face multiple barriers to virtual education participation and learning. While 12 qualitative studies were found, future research should aim to identify these aspects in low-income countries, as well as during the pandemic, and methods of overcoming the barriers described.
Type IV Pili: dynamic bacterial nanomachines
Authors: Ellison Courtney K , Whitfield Gregory B , Brun Yves V 
Published: November 2021

ABSTRACT
Bacteria and archaea rely on appendages called type IV pili (T4P) to participate in diverse behaviors including surface sensing, biofilm formation, virulence, protein secretion and motility across surfaces. T4P are broadly distributed fibers that dynamically extend and retract, and this dynamic activity is essential for their function in broad processes. Despite the essentiality of dynamics in T4P function, little is known about the role of these dynamics and molecular mechanisms controlling them. Recent advances in microscopy have yielded insight into the role of T4P dynamics in their diverse functions and recent structural work has expanded what is known about the inner workings of the T4P motor. This review discusses recent progress in understanding the function, regulation, and mechanisms of T4P dynamics.