bluuebunny/crossref_metadata_2025_split huggingface dataset:
Analysis of Physical and Chemical Conditions in Sidakarya Coastal Waters, Bali
Authors: Sufyan A , Akhwady R , Mahabror D , Permana S M , Zulkarnain R 
Published: December 2022

Abstract
Sidakarya Coast is one of the developing ecotourism and fisheries areas in Denpasar City, Bali Province. This area has ecotourism and fishery potential that needs to be maintained so that ecotourism and fishery activities that depend on this area can enjoy economic prosperity. Activities around the coast of Sidakarya, such as ecotourism, housing areas, traditional fisheries, and agriculture, have indirectly affected the quality of coastal waters. This research was one of the efforts to identify the physical and chemical parameters of the coastal waters, including, salinity, temperature, DO (Dissolved oxygen), water transparency and pH. This research was conducted in April 2021 with five measurement points of water quality factors. Measurement location determination using the purposive sampling method. Water quality analysis was carried out by comparing the measurement results with values of water quality standards based on the State Minister Decree of the Environment Number 51 of 2004 for marine tourism and marine biotas and reffering to the State Minister Decree of the Environment Number 115 of 2003 concerning Rules for determining the situation with quality of water. The measurement results showed the value of Sidakarya water quality parameters ranging from 30.2-30.6 °C for temperature, 0.6-5 meter for water transparency, 29.7-33.7°/oo for salinity, 4.94-7.04 mg/l for DO and 6.9-7.4 for pH. The results obtained that the condition of Sidakarya waters in general still meets the water quality; only the water transparency parameter at the location near the estuary was below the quality standard. The after effects of the estimation of the pollution index (PI) on each sampling station show the PI value <1 or meets the quality standards for marine biota (stations 1 and 2) and meet the quality standards for marine tourism (stations 3,4 and 5). The results indicated that Sidakarya waters can still be developed for ecotourism areas and limited fisheries.
Microplastic pollution in the surface water of Lake Singkarak, Indonesia
Authors: Henny C , Rohaningsih D , Suryono T , Santoso A B , Waluyo A 
Published: December 2022

Abstract
Microplastic pollution is already at an “alarming” level in Indonesia’s marine and freshwater ecosystems. However, to the best of our knowledge, no study has reported the microplastic occurrence in the lake ecosystem in Indonesia. Lake Singkarak, a big tectonic lake, has been considered one of the priority lakes to be restored. The lake receives a high influx of plastic waste from rivers and catchment runoff. Controlling the outflow through the hydropower dam and the sluice in the main lake outlet may prevent the microplastic’s outflux. The study’s objective was to determine the microplastic first occurrence and abundance in the lake’s surface water. Water samples were collected from three sites in the lake inlet area, one in the intake area of the hydropower dam and one in the outlet area, by performing four parallel trawls in each site using a modified plankton net. The most abundant microplastics in the lake’s surface water were 9 particles/m3 in the lake inlet area, which received a high plastic waste input from the river. The lowest abundance was 2 particles/m3 in the main lake outlet area. Foams and fragments, white and clear in color, size of 300 μm, were the dominant types of microplastics observed. Our preliminary study suggests that the lake could act as a sink of microplastics. Therefore, ceasing the input sources of plastic waste from the river should be prioritized to prevent further microplastic pollution of Lake Singkarak.
Performance Effectiveness of Communal Wastewater Treatment Plant as an Effort to Control Pollution of the Gajah Wong River, Yogyakarta
Authors: Pangestu M P , Rahmawati S , Sulistyo E N , Yulianto A , Budijono B 
Published: December 2022

Abstract
The Gajah Wong River receives wastewater from the high population of Sleman Regency, including agricultural activities and home industries that contain organic pollutants. High organic pollutants cause dissolved oxygen depletion in waters that can threaten the lives of various aquatic biota. The construction of a communal wastewater treatment plant (WWTP) for handling domestic wastewater is an effort to control river pollution. The effectiveness of WWTP performance based on key parameters is continuously monitored, which is the purpose of this research. Surveys on 4 (four) communal WWTPs (Ngudi Mulyo, Wahana Bina Lingkungan, Tirto Mili, and Karya Asri Ambarukmo) were conducted in February – April 2021 with the key parameters observed were pH, BOD5, COD, and NH3. Sampling wastewater by grab sampling at each inlet and outlet of the WWTP using ABR (Anaerobic Baffled Reactor) and RBC (Rotating Biological Contactor) technology 6 times. The results provide an overview of the quality characteristics of wastewater that has been treated (outlet) at the Ngundi Mulyo WWTP (NH3 16.55 mg/L, BOD5 32.53 mg/L, COD 213.52 mg/L, pH 5) Wahana Bina Lingkungan (NH3 29.85 mg/L, BOD5 262.36 mg/L, pH 6-7), Tirto Mulyo (NH3 20.42 mg/L, BOD5 66.67 mg/L, COD 248.7 mg/L, pH 6-7) and Karya Asri Ambarukmo (NH3 21.60 mg/L, BOD5 252.64 mg/L, pH 6-7). These results reveal that the performance of the four WWTPs is still low and has not been effective in reducing COD and NH3 parameters, except that BOD5 reaches the required quality standard, and the processed wastewater still has the potential to reduce the water quality of the Gajah Wong River. This result is also a signal for WWTP managers to improve the processing process in each of these WWTPs.
Tsunami Numerical Modelling in Ujung Kulon National Park with the Earthquake Magnitude Scenario of 6.5 and 6.9 Mw
Authors: Wijayanti R , Pasma G R , Nurwijayanti A , Rachman R A 
Published: December 2022

Abstract
Tsunami modelling was conducted to simulate tsunami events based on earthquake data previously occurring around Ujung Kulon National Park (TNUK), Banten Province using TUNAMI-F1 and TUNAMI-N3. TUNAMI-F1 is a modelling method to get the wave height and tsunami arrival time with a grid spacing of 0.00167°. While the TUNAMI-N3 is a model that applies the theory of wave propagation linearly in a grid variation to get a high output of tsunami inundation. The tsunami source data was used from historical earthquake generation on January 14, 2022 (6.5 Mw) and August 2, 2019 (6,9 Mw). The reverse fault type scenario from Wells & Coppersmith (1994) is used to calculate the scaling law with length, width, and the focal mechanism value obtained from the United States Geological Survey (USGS) to generate initial waves based on the multideform model. The TUNAMI-N3 model applies a nested model with variations in grid spacing and the most detailed value is 68,556 m. The tsunami wave height based on the magnitude 6.5 Mw scenario is around 0.001 m to 0.05 m with the highest wave height found on the southern coast of TNUK and the southern coastal area of Peucang Island (0.03-0.05m). The inundation produced is only visible in the E1 domain reaching 96-192 m in areas A, B, C. Then, the maximum inundation area is the south coast of TNUK (0.01-0.03m). Based on the second scenario, the height of the tsunami waves generated is in the range of 0.001 − 0.3 m. The maximum tsunami height was in the Rancecet Beach area, south of Tinjil Island, the south, east, and north coasts of TNUK (0.03-0.3m). The run-up distance resulting from scenario 1 is less than 1 km. Based on TUNAMI-F1 model results, wave height maximum caused by 6.5 Mw magnitude is higher than 6.9 Mw.
An experimental study of friction stir welding parameters effect on joint properties of aluminium alloy and copper plate
Authors: Baghel Surjeet Singh , Soni Pradeep Kumar 
Published: December 2022

Abstract
Joining dissimilar metals like copper and aluminium is a complex area of research for the manufacturing industry. To effectively join the AA7075 with copper plates, an experimental investigation on friction stir welding was carried out. A straight cylindrical pin profile tool of H13 tool steel was chosen for this study. On the advancing direction, the AA7075 plates were fixed under the condition of zero tool offset. The tool was positioned at a 2° tilt angle for the entire experiment. Tensile test, microhardness test, SEM and EDS analysis were completed to investigate the effectiveness of the process parameters (tool traverse and rotational speed) in combination with a modified set-up on the microstructure, tensile strength and microhardness of the joint. Fractography was conducted on fractured specimens to identify the mode of failure. Complex microstructures of swirl and vortex-type material flow patterns were created in the stir zone. As a result of SEM analysis, one of the samples (S5) had finer grains at intermediate heat input, which produced excellent microhardness and tensile strength. Fractography identified ductile failure as the predominant mode of failure in the joints. The results of this study include an ultimate tensile strength value of 221.091 MPa with a joint efficiency of 95.05%, yield strength of 159.035 MPa, maximum elongation of 9.335% and a microhardness value of 271 HV for specimen welded at a traverse speed of 60 mm min−1 and a rotational speed of 1400 rpm.
A Dynamic Risk Model for Multitype Recurrent Events
Authors: Ghosh Alokananda , Chan Wenyaw , Younes Naji , Davis Barry R 
Published: December 2022

Abstract
Recurrent events can occur more than once in the same individual; such events may be of different types, known as multitype recurrent events. They are very common in longitudinal studies. Often there is a terminating event, after which no further events can occur. The risk of any event, including terminating events such as death or cure, is typically affected by prior events. We propose a flexible joint multitype recurrent-events model that explicitly provides estimates of the change in risk for each event due to subject characteristics, including number and type of prior events and the absolute risk for every event type (terminating and nonterminating), and predicts event-free survival probability over a desired time period. The model is fully parametric, and therefore a standard likelihood function and robust standard errors can be constructed. We illustrate the model with applications to the Antihypertensive and Lipid-Lowering Treatment to Prevent Heart Attack Trial (1994–2002) and provide discussion of the results and model features.
Optimally Choosing Medication Type for Patients With Opioid Use Disorder
Authors: Rudolph Kara E , Williams Nicholas T , Díaz Iván , Luo Sean X , Rotrosen John , Nunes Edward V 
Published: December 2022

AbstractPatients with opioid use disorder (OUD) tend to get assigned to one of 3 medications based on the treatment program to which the patient presents (e.g., opioid treatment programs tend to treat patients with methadone, while office-based practices tend to prescribe buprenorphine). It is possible that optimally matching patients with treatment type would reduce the risk of return to regular opioid use (RROU). We analyzed data from 3 comparative effectiveness trials from the US National Institute on Drug Abuse Clinical Trials Network (CTN0027, 2006–2010; CTN0030, 2006–2009; and CTN0051 2014–2017), in which patients with OUD (n = 1,459) were assigned to treatment with either injection extended-release naltrexone (XR-NTX), sublingual buprenorphine-naloxone (BUP-NX), or oral methadone. We learned an individualized rule by which to assign medication type such that risk of RROU during 12 weeks of treatment would be minimized, and then estimated the amount by which RROU risk could be reduced if the rule were applied. Applying our estimated treatment rule would reduce risk of RROU compared with treating everyone with methadone (relative risk (RR) = 0.79, 95% confidence interval (CI): 0.60, 0.97) or treating everyone with XR-NTX (RR = 0.71, 95% CI: 0.47, 0.96). Applying the estimated treatment rule would have resulted in a similar risk of RROU to that of with treating everyone with BUP-NX (RR = 0.92, 95% CI: 0.73, 1.11).
Endogenous Steroid Hormone Concentrations and Risk of Endometriosis in Nurses’ Health Study II
Authors: Shafrir Amy L , Mu Fan , Eliassen A Heather , Thombre Kulkarni Madhavi , Terry Kathryn L , Hankinson Susan E , Missmer Stacey A 
Published: December 2022

Abstract
Few studies have assessed the association between endogenous steroid hormone levels and a subsequent diagnosis of endometriosis. We prospectively evaluated premenopausal plasma sex hormone levels and the risk of laparoscopically confirmed endometriosis in a nested case-control study within Nurses’ Health Study II. Between blood collection (1996–1999) and 2009, we ascertained 446 women with incident endometriosis and matched them to 878 controls through risk-set sampling. We conducted multivariable conditional logistic regression accounting for matching and confounders to estimate relative risks (RRs) and 95% confidence intervals (CIs). Women with greater early follicular-phase total or free estradiol levels had a nonlinear increased risk of endometriosis (early follicular total estradiol: second quartile vs. first, RR = 2.23 (95% CI: 1.44, 3.47); third quartile, RR = 1.83 (95% CI: 1.16, 2.88); fourth quartile, RR = 1.68 (95% CI: 1.05, 2.68); early follicular free estradiol: second quartile vs. first, RR = 1.63 (95% CI: 1.05, 2.54); third quartile, RR = 2.02 (95% CI: 1.31, 3.12); fourth quartile, RR = 1.04 (95% CI: 0.66, 1.65)). Free testosterone assessed in quartile categories was not associated with endometriosis, although a threshold effect was observed, with a positive association among women in the top 2% of free testosterone levels. Levels of mid–luteal-phase total and free estradiol, follicular and luteal estrone, total testosterone, progesterone, and sex hormone binding globulin were not associated with endometriosis risk. These results support the role of sex steroids in endometriosis etiology, although the relationships suggest complex threshold effects.
Bias Amplification and Variance Inflation in Distributed Lag Models Using Low-Spatial-Resolution Data
Authors: Leung Michael , Rowland Sebastian T , Coull Brent A , Modest Anna M , Hacker Michele R , Schwartz Joel , Kioumourtzoglou Marianthi-Anna , Weisskopf Marc G , Wilson Ander 
Published: December 2022

Abstract
Distributed lag models (DLMs) are often used to estimate lagged associations and identify critical exposure windows. In a simulation study of prenatal nitrogen dioxide (NO2) exposure and birth weight, we demonstrate that bias amplification and variance inflation can manifest under certain combinations of DLM estimation approaches and time-trend adjustment methods when using low-spatial-resolution exposures with extended lags. Our simulations showed that when using high-spatial-resolution exposure data, any time-trend adjustment method produced low bias and nominal coverage for the distributed lag estimator. When using either low- or no-spatial-resolution exposures, bias due to time trends was amplified for all adjustment methods. Variance inflation was higher in low- or no-spatial-resolution DLMs when using a long-term spline to adjust for seasonality and long-term trends due to concurvity between a distributed lag function and secular function of time. NO2–birth weight analyses in a Massachusetts-based cohort showed that associations were negative for exposures experienced in gestational weeks 15–30 when using high-spatial-resolution DLMs; however, associations were null and positive for DLMs with low- and no-spatial-resolution exposures, respectively, which is likely due to bias amplification. DLM analyses should jointly consider the spatial resolution of exposure data and the parameterizations of the time trend adjustment and lag constraints.
Patterns of extra-territorial nest-box visits in a songbird suggest a role in extrapair mating
Authors: Santema Peter , Kempenaers Bart 
Published: December 2022

Abstract
Many animals make visits outside of their territory during the breeding period, but these are typically infrequent and difficult to observe. As a consequence, comprehensive data on extra-territorial movements at the population-level are scarce and the function of this behavior remains poorly understood. Using an automated nest-box visit tracking system in a wild blue tit population over six breeding seasons, we recorded all extra-territorial nest-box visits (n = 22 137) related to 1195 individual breeding attempts (761 unique individuals). Sixty-two percent of breeders made at least one extra-territorial visit between the onset of nest building and the day of fledging of their offspring, and individuals visited another nest-box on average on 11% of the days during this period. Visit behavior differed clearly between the sexes, with males making over three times as many extra-territorial forays as females. There was a strong overall seasonal decline in visit behavior, but this was sex dependent, with females showing a strong reduction in the number of extra-territorial visits before the onset of egg laying and males showing a strong and sudden reduction on the day their offspring hatched. The likelihood of visiting a particular nest-box declined sharply with the distance to that box, and blue tits almost exclusively visited direct neighbors. Individuals were more likely to have extrapair offspring with an individual whose box they visited, but they were not more likely to disperse to a box they had visited. Thus, our results are inconsistent with the hypothesis that extra-territorial nest-box visits serve to inform dispersal decisions, but suggest that such visits are linked to extrapair mating opportunities.
Attentive Variational Information Bottleneck for TCR–peptide interaction prediction
Authors: Grazioli Filippo , Machart Pierre , Mösch Anja , Li Kai , Castorina Leonardo V , Pfeifer Nico , Min Martin Renqiang 
Published: December 2022

Abstract

Motivation
We present a multi-sequence generalization of Variational Information Bottleneck and call the resulting model Attentive Variational Information Bottleneck (AVIB). Our AVIB model leverages multi-head self-attention to implicitly approximate a posterior distribution over latent encodings conditioned on multiple input sequences. We apply AVIB to a fundamental immuno-oncology problem: predicting the interactions between T-cell receptors (TCRs) and peptides.

Results
Experimental results on various datasets show that AVIB significantly outperforms state-of-the-art methods for TCR–peptide interaction prediction. Additionally, we show that the latent posterior distribution learned by AVIB is particularly effective for the unsupervised detection of out-of-distribution amino acid sequences.

Availability and implementation
The code and the data used for this study are publicly available at: https://github.com/nec-research/vibtcr.

Supplementary information
Supplementary data are available at Bioinformatics online.
Tamoxifen improves muscle structure and function of Bin1- and Dnm2-related centronuclear myopathies
Authors: Gineste Charlotte , Simon Alix , Braun Marie , Reiss David , Laporte Jocelyn 
Published: December 2022

Abstract
Congenital myopathies define a genetically heterogeneous group of disorders associated with severe muscle weakness, for which no therapies are currently available. Here we investigated the repurposing of tamoxifen in mouse models of mild or severe forms of centronuclear myopathies due to mutations in BIN1 (encoding amphiphysin 2) or DNM2 (encoding dynamin 2), respectively. Exposure to a tamoxifen-enriched diet from 3 weeks of age resulted in significant improvement in muscle contractility without increase in fibre size in both models, underlying an increase in the capacity of the muscle fibres to produce more force. In addition, the histological alterations were fully rescued in the BIN1-centronuclear myopathies mouse model. To assess the mechanism of the rescue, transcriptome analyses and targeted protein studies were performed.
Although tamoxifen is known to modulate the transcriptional activity of the oestrogen receptors, correction of the disease transcriptomic signature was marginal on tamoxifen treatment. Conversely, tamoxifen lowered the abnormal increase in dynamin 2 protein level in both centronuclear myopathies models. Of note, it was previously reported that dynamin 2 increase is a main pathological cause of centronuclear myopathies. The Akt/mTOR muscle hypertrophic pathway and protein markers of the ubiquitin–proteasome system (the E3 ubiquitin ligase cullin 3) and autophagy (p62) were increased in both models of centronuclear myopathies. Normalization of dynamin 2 level mainly correlated with the normalization of cullin 3 protein level on tamoxifen treatment, supporting the idea that the ubiquitin–proteasome system is a main target for the tamoxifen effect in the amelioration of these diseases. Overall, our data suggest that tamoxifen antagonizes disease development probably through dynamin 2 level regulation. In conclusion, the beneficial effect of tamoxifen on muscle function supports the suggestion that tamoxifen may serve as a common therapy for several autosomal forms of centronuclear myopathies.
Neurocomputational mechanisms of young children’s observational learning of delayed gratification
Authors: Zhao Hui , Zhang Tengfei , Cheng Tong , Chen Chuansheng , Zhai Yu , Liang Xi , Cheng Nanhua , Long Yuhang , Li Ying , Wang Zhengyan , Lu Chunming 
Published: December 2022

AbstractThe ability to delay gratification is crucial for a successful and healthy life. An effective way for young children to learn this ability is to observe the action of adult models. However, the underlying neurocomputational mechanism remains unknown. Here, we tested the hypotheses that children employed either the simple imitation strategy or the goal-inference strategy when learning from adult models in a high-uncertainty context. Results of computational modeling indicated that children used the goal-inference strategy regardless of whether the adult model was their mother or a stranger. At the neural level, results showed that successful learning of delayed gratification was associated with enhanced interpersonal neural synchronization (INS) between children and the adult models in the dorsal lateral prefrontal cortex but was not associated with children’s own single-brain activity. Moreover, the discounting of future reward’s value obtained from computational modeling of the goal-inference strategy was positively correlated with the strength of INS. These findings from our exploratory study suggest that, even for 3-year-olds, the goal-inference strategy is used to learn delayed gratification from adult models, and the learning strategy is associated with neural interaction between the brains of children and adult models.