bluuebunny/crossref_metadata_2025 huggingface dataset:
Identification of bacterial communities related to handling in commercial white-leg shrimp (Litopenaeus vannamei) using metagenomic analysis
Authors: Abdullah A , Pratama R , Sauqi S D A , Nurhayati T , Sofyan
Published: February 2023

Post-harvest handling, which includes the use of cold chains and proper hygiene, plays a critical role in maintaining fish quality and food safety. The bacterial community in white-leg shrimp will be affected by differences in the level of hygiene used in traditional and modern markets. This study was aimed to isolate bacterial DNA and identify bacterial communities on the surface of shrimps sold in the commercial market using metagenomic analysis. The research methods covered the isolation of bacterial DNA followed by the metabarcoding analysis of 16S rRNA and bioinformatics analysis. The sequence abundance of bacteria in White-leg shrimp samples were dominated by the genusMyroides, with a relative abundance of 49.18% in traditional markets and 84.89% in modern markets. Bacterial DNA from the skin surface of shrimp from traditional and modern markets has been isolated. The samples of shrimp from traditional markets had a higher relative abundance and diversity of bacteria than samples from modern markets.
The evaluation of antioxidant action of green seaweed Boergesenia forbesii extracts
Authors: Gazali M , Husni A , Majid F A A , Zuriat  , Syafitri R , Wahyuni S , Hidayat D
Published: February 2023

Boergesenia forbesii is green seaweed in the intertidal Zone of West Aceh that widely distributed in certain season. This study aimed to analyze the activity of antioxidant in green seaweed B. forbesii extract. The samples of B. forbesii were obtained from Intertidal Zone of West Aceh. Subsequently, a vacuum rotary evaporator extracted three solvents based on polarity including methanol, ethyl acetate, and n-hexane solvents. The experimental assays consisted of phytochemical, DPPH antioxidant activity and total phenolic content. The result revealed that the methanol extract (6.26%) yielded the highest rendement, then followed by ethyl acetate extract (4.03%) and n-hexane (0.56%). B. forbesii crude extract have already been detected in phenolic, flavonoid, saponin and steroid compounds. The antioxidant activity measurement with DPPH method indicated that the ethyl acetate extract had higher activity (53.10 mg/L) than methanol crude extract (79.4 mg/L) and n-hexane extract (378.3±0.028 mg/L). It is corroborated with the correlation of TPC and antioxidant activity indicating 99% of scavenging of free radical activity is caused by phenolic groups. The pharmaceutical industry can used in antioxidant agents.
The effectivity of probiotic containing Bacillus spp. applicated in the rearing of mud crab Scylla tranquebarica larvae to produce crablet
Authors: Gunarto  , Herlinah  , Sulaeman  , Muliani  , Tampangalo B R
Published: February 2023

Probiotic bacteria in larvae rearing is expected to suppress pathogenic bacteria and improve water quality. The research aimed to determine the effectivity of probiotic bacteria containing Bacillus subtilis and B. licheniformis on larval rearing of purple mud crab Scylla tranquebarica to produce crablet. The larvae were stocked in nine units of conical fiber tank, fed Rotifers, Brachionus plicatilis, and nauplii Artemia sp. The probiotics tested, namely, A). RICA-4, containing the bacterium Bacillus subtilis, B). RICA-5 containing B. licheniformis, C). A combination of probiotics RICA-4 and RICA-5. The administration of each probiotic with a density of 108 CFU g−1 (5 mg L−1) was given to the water media for larvae rearing. The lowest nitrite and Total Organic Matter in the zoea stage were found in treatment B. At the megalopa stage, treatment B’s lowest TOM concentration occurred and was significantly different (p<0.05) from treatment C. On the other hand, the highest population of Vibrio spp (5.5x103 CFU mL−1) was obtained in treatment A. In contrast, treatment C had the highest bacteria population (4.8x104 CFU mL-1). On day 19, the megalopa in treatment B was more abundant than in treatments A and C causing crablet production in treatment B (280.5±47.50 ind. tank −1) was significantly higher (p<0.05) than crablet production in treatment C (196.5±29.50 ind. tank −1) and A (161.0±21.00 ind. tank −1). Therefore, improving water quality in treatment B may have an important factor in enhancing crablet production.
Mangrove species structure at the Tuntang Estuary, Demak, Central Java
Authors: Rahim A , Soeprobowati T R , Putranto T T
Published: February 2023

The Tuntang estuary is located in the coastal area of the Demak Regency, which has a considerable mangrove ecosystem potential. However, their persistence is degraded due to land conversion, deforestation, and climate change. Hence, to provide the basis for mangrove conservation in that area, it is essential to gain insight into the mangroves’ composition and structure. Vegetation data were obtained by using a quadratic transect survey method with plot sizes for categories of the tree (10x10 m), sapling (5x5 m), and seedling (2x2 m). The results showed that eleven true mangroves and three mangrove-associated species were found in the mangrove ecosystem of the Tuntang estuary. All true mangrove species are included in the International Union for Conservation of Nature and Natural Resources (IUCN) Red List of threatened species. The dominant species was Rhizophora mucronata, which showed the most significant important value index of each growth stage. The research area’s biodiversity and dominance index were categorized as very low, but the evenness index was relatively high. The standing structure in the reverse “J” shape is formed by the number of trees and regeneration ratios. The vulnerability to degradation level on density and dominance index parameters was low, while the diversity index parameter was classified as moderate, which displays a potential vulnerability to disturbances. This study highlights that conserving mangrove ecosystems on the coast around the Tuntang estuary is essential to defend the coastal area from abrasion and tidal flooding, which have been problems in the area for long periods.
Seagrass diversity and dugong observation in North Minahasa Regency, North Sulawesi
Authors: Meidina T S A , Kamal M M , Kurniawan F , Darusman H S , Digdo A A
Published: February 2023

Dugong is a marine mammal that only eats seagrass. Feeding tracks of dugongs in the seagrass beds indicate their presence. The dugong population is currently experiencing a decline due to habitat destruction and other anthropogenic factors. This study aimed to determine the seagrass diversity and their relationship to the presence of dugongs. The research was conducted in villages of Bahoi, Tarabitan, Bulutui, and Gangga I Island using the seagrass-watch method. Analysis of the data used was the percentage of seagrass cover, density of seagrass species, and indicators of the presence of seagrass, which was carried out by interviewing fishermen and surveying their feeding tracks. The results showed that the waters in the North Minahasa Regency had seven seagrass types. The average percentage of seagrass cover was 61.73% and the density of seagrass species was 766.88 shoots/m2. Feeding tracks observed in three locations, in Bahoi, Tarabitan, and Bulutui villages. The most tracks of feeding tracks were in Bahoi Village, with the type of seagrass that dominated being eaten by dugongs was Halodule pinifolia. Based on the results obtained, it concluded that certain types of seagrass are related to the location of the emergence of dugongs in the North Minahasa Regency.
The abundance of coral diseases and compromise health in marine protected areas on Dampier waters, Raja Ampat
Authors: Johan O , Idris
Published: February 2023

The extent of coral reefs, coral biodiversity, and associated biota are known as high mega biodiversity in Indonesian waters, in other words, The Coral Triangle. Threats of coral damage have also been widely reported, including deaths due to natural factors. Coral disease is a natural factor that is not widely known for its existence around Indonesian waters. This study was conducted to obtain the abundance of coral disease by using a belt transect method of 20 m long with a width of 50 cm to the left and right of the transect line, then carried out three replications at ten observation stations in Dampier waters, Raja Ampat. The study obtained data on the abundance of coral diseases that infect eight coral genera ranging from 0-23 col/60 m2, the highest station at station 8 (23 col/60 m2). There were six types of coral disease found in the Dampier Strait MPA, including WS, BrBD, FB, AtN, Bleaching, and Tumor. The highest abundance was found in WS disease (65 col/60m2). Coral health confounding factors were found in 336 colonies with abundance at different stations ranging from 14 – 97 col/60 m2. The highest abundance was found at station 5 (97 col/60 m2), a high stressor due to being located at sub-zona Sasi and traditional use. The existence of the disease is not classified as an outbreak. However, it is necessary to be careful if there is an increase in the number of new infection cases in the exact location or other places in Indonesia.
Social, economic, and institutional assessments of thresher shark (Alopias pelagicus) fisheries management at Kutaraja Ocean Fishing Port, Banda Aceh: an ecosystem approach
Authors: Mardhatillah I , Taurusman A A , Sondita M F A
Published: February 2023

The pelagic thresher shark (Alopias pelagicus) is the dominant bycatch that landed at the Kutaraja Ocean Fishing Port. This species has been considered endangered and listed under CITES Appendix II. Some fishers of purse seiners and handliners from Kutaraja Fishing Port catch the thresher sharks, but the catch is considered the bycatch of these types of fishing fleets. These fishing practices have promoted conflict among fishers and illegal fishing practices and reduced the income of the fishers. This study aims to assess the management status of A. pelagicus fishery involving the purse seiners and handliners by EAFM framework; and to formulate management measures promoting the sustainability of the shark population based on social, economic, and institutional aspects. This research was conducted through field measurement and interviews with key stakeholders. A composite index technique analyzed data in frame of EAFM. The social aspect of the fisheries management showed a ‘very good’ status (score of 83.3%), while the economic aspect was of ‘good’ category (score of 66.7%) and the institutional governance aspect was of ‘poor’ category (score of 33.3%). Thus, the institutional aspect of management needs to be improved to achieve sustainability of the pelagic thresher shark fishery in terms of socio-economic and governance. This study recommends the implementation of a profit-sharing system as regulated by the government, implementing local wisdom related to fisheries, reducing sharks for local consumption and trading, formulating sustainable shark policy, providing facilities and conducting regular monitoring action for shark fisheries.
Population Dynamic Parameters and Length Based Spawning Potential Ratio (LB-SPR) of Red Snapper (Lutjanus malabaricus) in The Eastern Java Sea
Authors: Hapsari A D , Zairion  , Kamal M M , Kosasih G , Saputra A
Published: February 2023

Decision in fisheries management must be made based on the best scientific evidence available. In the poor data fisheries, the fish length data can be useful to determine the status of fish population after its exploitation. The target species of the studied fisheries is the red snapper (Lutjanus malabaricus) in the eastern Java Sea. This study aims to analyze the stock status of red snapper in the eastern Java Sea using Length Based Spawning Potential Ratio (LB-SPR) method. Data collection was done from November 2020 until April 2021. This study separated the analysis of the population dynamic parameters between male and female fish. The growth parameters of male fish was Lt = 92.20 (1 – e−0.27(t-0.07)), with natural mortality (M) of 0.35, fishing mortality (F) of 0.63, and total mortality (Z) of 0.98 per-year. Whereas for female fish, Lt = 91.09 (1 – e−0.29(t-0.44)), with M of 0.38, F of 1.40, and Z of 1.78. The exploitation rate (E) for males was 0.64, and for the female was 0.79. The spawning potential ratio (SPR) was 17%, below the limit reference point of 30% SPR. The current utilization rate of the red snapper in the eastern Java Sea must be reduced to ensure its sustainability.
Spin–orbit and exchange proximity couplings in graphene/1T-TaS2 heterostructure triggered by a charge density wave
Authors: Szałowski Karol , Milivojević Marko , Kochan Denis , Gmitra Martin
Published: February 2023

Proximity-induced fine features and spin-textures of the electronic bands in graphene-based van der Waals heterostructures can be explored from the point of tailoring a twist angle. Here we study spin–orbit coupling and exchange coupling engineering of graphene states in the proximity of 1T-TaS2 not triggering the twist, but a charge density wave (CDW) in 1T-TaS2—a realistic low-temperature phase. Using density functional theory and effective model we found that the emergence of the CDW in 1T-TaS2 significantly enhances Rashba spin–orbit splitting in graphene and tilts the spin texture by a significant Rashba angle—in a very similar way as in the conventional twist-angle scenarios. Moreover, the partially filled Ta d-band in the CDW phase leads to the spontaneous emergence of the in-plane magnetic order that transgresses via proximity from 1T-TaS2 to graphene, hence, simultaneously superimposing along the spin–orbit also the exchange coupling proximity effect. To describe this intricate proximity landscape we have developed an effective model Hamiltonian and provided a minimal set of parameters that excellently reproduces all the spectral features predicted by the first-principles calculations. Conceptually, the CDW provides a highly interesting knob to control the fine features of electronic states and to tailor the superimposed proximity effects—a sort of twistronics without twist.
A novel and predictive process of manufacturing 3DN C/SiC torque tube
Authors: Zhao Hui , Zhang Jiaxin
Published: February 2023

In this research, a novel method of CVI + RMI 3DN C/SiC torque tube preparation has been researched. CVI + RMI 3DN C/SiC flat panel was evaluated by Archimedes drainage method for density and open porosity, SEM for morphological characterization, XRD for phase composition characterization, and chemical method for composition mass and volume content. It has an average density of 2.19 g cm−3, and open porosity of 10%. The computed chemical composition method findings are undoubtedly in line with the fiber design volume percentage of 30%. Tensile and shear mechanical tests on 3DN C/SiC standard sample were investigated, with good performance. The average tensile and shear strength was 141.64 MPa and 86.24 MPa respectively. 3DN C/SiC torque tubes were prepared by the same process, and the torsional mechanical tests were carried out. According to the mechanical parameters of the flat panel 3DN C/SiC sample, the mechanical properties of stress distribution and shear stress-strain curves for the torque tube are predicted by using the finite element simulation method, which is in good agreement with the test results. The test and simulation error of the maximum shear strength is only about 2%.
Key issues in microstructure modeling of 3D braided composites
Authors: Wang Zhen , Liu Shuai , Zhao Zhigao , Liu Fang , Zhang Hui , Shen Min
Published: February 2023

Numerical analysis based on micromechanics is an effective method to study the mechanical properties of three-dimensional (3D) braided composites, in which the establishment of micromechanics model is the basis of mechanical analysis. The direction cosine of fiber yarns and the characterization of geometric parameters of microstructure are two key issues in the modeling of microstructure. Focusing on these two key issues, the three-cell model of 3D four-directional braided composites are studied to comprehensively analyze various spatial directions of fiber yarns in the 45° division and horizontal division of unit cell, so as to obtain the detailed fiber yarn direction cosine. Aiming at the cross sections of three types of fiber yarns, the complex relationship between the braiding process parameters and the geometric parameters of the unit cell is analyzed and deduced. The unit cell structure is quantitatively characterized by using the braiding process parameters as the initial parameters, and the calculation methods of the volume fraction of fiber yarns and yarn filling coefficient are obtained. Finally, the predicted elastic constants by stiffness-volume averaging method are compared with experimental results, demonstrating the analysis results of fiber yarns directions. This paper can provide a theoretical reference for the microstructure modeling of 3D multi-directional braided composites, and has certain practical value in engineering.
Robust simulation-based inference in cosmology with Bayesian neural networks
Authors: Lemos Pablo , Cranmer Miles , Abidi Muntazir , Hahn ChangHoon , Eickenberg Michael , Massara Elena , Yallup David , Ho Shirley
Published: February 2023

Simulation-based inference (SBI) is rapidly establishing itself as a standard machine learning technique for analyzing data in cosmological surveys. Despite continual improvements to the quality of density estimation by learned models, applications of such techniques to real data are entirely reliant on the generalization power of neural networks far outside the training distribution, which is mostly unconstrained. Due to the imperfections in scientist-created simulations, and the large computational expense of generating all possible parameter combinations, SBI methods in cosmology are vulnerable to such generalization issues. Here, we discuss the effects of both issues, and show how using a Bayesian neural network framework for training SBI can mitigate biases, and result in more reliable inference outside the training set. We introduce cosmoSWAG, the first application of stochastic weight averaging to cosmology, and apply it to SBI trained for inference on the cosmic microwave background.
Prognostic Value of Low-Pass Whole Genome Sequencing of Circulating Tumor DNA in Metastatic Castration-Resistant Prostate Cancer
Authors: Nørgaard Maibritt , Bjerre Marianne T , Fredsøe Jacob , Vang Søren , Jensen Jørgen B , De Laere Bram , Grönberg Henrik , Borre Michael , Lindberg Johan , Sørensen Karina D
Published: February 2023

Background

Multiple treatments are available for metastatic castration-resistant prostate cancer (mCRPC), including androgen receptor signaling inhibitors (ARSI) enzalutamide and abiraterone, but therapy resistance remains a major clinical obstacle. We examined the clinical utility of low-pass whole-genome sequencing (LPWGS) of circulating tumor DNA (ctDNA) for prognostication in mCRPC.

Methods

A total of 200 plasma samples from 143 mCRPC patients collected at the start of first-line ARSI treatment (baseline) and at treatment termination (n = 57, matched) were analyzed by LPWGS (median: 0.50X) to access ctDNA% and copy number alteration (CNA) patterns. The best confirmed prostate specific antigen (PSA) response (≥50% decline [PSA50]), PSA progression-free survival (PFS), and overall survival (OS) were used as endpoints. For external validation, we used plasma LPWGS data from an independent cohort of 70 mCRPC patients receiving first-line ARSI.

Results

Baseline ctDNA% ranged from ≤3.0% to 73% (median: 6.6%) and CNA burden from 0% to 82% (median: 13.1%) in the discovery cohort. High ctDNA% and high CNA burden at baseline was associated with poor PSA50 response (P = 0.0123/0.0081), poor PFS (P < 0.0001), and poor OS (P < 0.0001). ctDNA% and CNA burden was higher at PSA progression than at baseline in 32.7% and 42.3% of the patients. High ctDNA% and high CNA burden at baseline was also associated with poor PFS and OS (P ≤ 0.0272) in the validation cohort.

Conclusions

LPWGS of ctDNA provides clinically relevant information about the tumor genome in mCRPC patients. Using LPWGS data, we show that high ctDNA% and CNA burden at baseline is associated with short PFS and OS in 2 independent cohorts.
Deconvolution of BNP and NT-proBNP Immunoreactivities by Mass Spectrometry in Heart Failure and Sacubitril/Valsartan Treatment
Authors: Nougué Hélène , Michel Thibault , Picard François , Lassus Johan , Sadoune Malha , Laribi Said , Cohen-Solal Alain , Logeart Damien , Launay Jean-Marie , Vodovar Nicolas
Published: February 2023

Background

Elevated BNP and the N-terminal fragment of the proBNP (NT-proBNP) are hallmarks of heart failure (HF). Generally, both biomarkers parallel each other. In patients receiving sacubitril/valsartan, BNP remained stable while NT-proBNP decreased. As BNP and NT-proBNP assays have limited specificity due to cross-reactivity, we quantified by mass spectrometry (MS) the contributing molecular species.

Methods

We included 356 healthy volunteers, 100 patients with acute dyspnoea (49 acute decompensated HF; 51 dyspnoea of non-cardiac origin), and 73 patients with chronic HF and reduced ejection fraction treated with sacubitril/valsartan. BNP and NT-proBNP immunoreactivities (BNPir and NT-proBNPir) were measured by immunoassays (Abbott ARCHITECT and Roche Diagnostics proBNPII) and proBNP-derived peptides and glycosylation at serine 44 by MS on plasma samples.

Results

BNPir corresponded to the sum of proBNP1–108, BNP1–32, BNP3–32, and BNP5–32 (R2 = 0.9995), while NT-proBNPir corresponded to proBNP1–108 and NT-proBNP1–76 not glycosylated at serine 44 (R2 = 0.992). NT-proBNPir was better correlated (R2 = 0.9597) than BNPir (R2 = 0.7643) with proBNP signal peptide (a surrogate of proBNP production). In patients receiving sacubitril/valsartan, non-glycosylated NT-proBNP1–76 remained constant (P = 0.84) despite an increase in NT-proBNP1–76 and its glycosylation (P < 0.0001). ProBNP1–108 remained constant (P = 0.12) while its glycosylation increased (P < 0.0001), resulting in a decrease in non-glycosylated proBNP1–108 (P < 0.0001), and in NT-proBNPir.

Conclusions

Glycosylation interfered with NT-proBNPir measurement, explaining the discrepant evolution of these 2 biomarkers in patients receiving sacubitril/valsartan. Both BNPir and NT-proBNPir are surrogates of proBNP1–108 production, NT-proBNPir being more robust in the clinical contexts studied.
Intergenerational effects of parental unemployment on infant health: evidence from Swedish register data
Authors: Högberg Björn , Baranowska-Rataj Anna , Voßemer Jonas
Published: February 2023

Parental unemployment can have detrimental effects on life chances of the children, and thereby reinforce inequalities across generations. Despite a substantial literature documenting that the health of infants at birth can have large and long-lasting consequences, research on intergenerational unemployment effects on infant health is scant. This study fills the gap using high-quality register data from Sweden, including 1.5 million siblings born between 1996 and 2017. To account for selection into unemployment, we employ sibling comparison designs that exploit variation in siblings’ exposure to parental unemployment, thereby accounting for stable but unmeasured confounding at the level of families. We find small and not consistently significant effects of maternal unemployment, and no effects of paternal unemployment. Our results also suggest that pre-existing social disadvantages—low education, migration background, and dual parental unemployment—are not associated with more adverse intergenerational unemployment effects. The discussion of our findings situates these results in the context of a relatively generous and egalitarian welfare state.
Occupational role and COVID-19 among foreign-born healthcare workers in Sweden: a registry-based study
Authors: Nwaru Chioma , Li Huiqi , Bonander Carl , Santosa Ailiana , Franzén Stefan , Rosvall Maria , Nyberg Fredrik
Published: February 2023

Background

Many studies report that foreign-born healthcare workers (HCWs) in high-income countries have an elevated risk of COVID-19. However, research has not yet specifically evaluated the distribution of COVID-19 among foreign-born workers in different healthcare work groups. We examined the risk of COVID-19 infection and hospitalization among foreign-born HCWs in different occupational roles in Sweden.

Methods

We linked occupational data (2019) of 783 950 employed foreign-born workers (20–65 years) to COVID-19 data registered between 1 January 2020 and 30 September 2021. We used Cox proportional hazards regression to estimate the hazard ratio (HR) with 95% confidence intervals (95% CIs) of COVID-19 infection and hospitalization in eight healthcare occupational groups vs. non-HCWs and assessed whether region of birth modified the association between healthcare occupations and COVID-19.

Results

All HCWs had a higher risk of COVID-19 outcomes than non-HCWs, but the risk differed by occupational role. Hospital-based assistant nurses had the highest risk (infection: HR 1.78; 95% CI 1.72–1.85; hospitalization: HR 1.79; 95% CI 1.52–2.11); allied HCWs had the lowest risk (infection: HR 1.22; 95% CI 1.10–1.35; hospitalization: HR 0.98; 95% CI 0.59–1.63). The relative hazard of the outcomes varied across foreign-born workers from different regions. For example, the relative risk of COVID-19 infection associated with being a physician compared to a non-HCW was 31% higher for African-born than European-born workers.

Conclusions

The risk of COVID-19 among foreign-born HCWs differed by occupational role and immigrant background. Public health efforts that target occupational exposures as well as incorporate culturally responsive measures may help reduce COVID-19 risk among foreign-born HCWs.
A Genetically Heterogeneous Rat Model with Divergent Mitochondrial Genomes
Authors: Sathiaseelan Roshini , Ahn Bumsoo , Stout Michael B , Logan Sreemathi , Wanagat Jonathan , Nguyen Hoang Van M , Hord Norman G , Vandiver Amy R , Selvarani Ramasamy , Ranjit Rojina , Yarbrough Hannah , Masingale Anthony , Miller Benjamin F , Wolf Roman F , Austad Steven N , Richardson Arlan
Published: February 2023

We generated a genetically heterogenous rat model by a 4-way cross strategy using 4 inbred strains (Brown Norway [BN], Fischer 344 [F344], Lewis [LEW], and Wistar Kyoto [KY]) to provide investigators with a highly genetically diverse rat model from commercially available inbred rats. We made reciprocal crosses between males and females from the 2 F1 hybrids to generate genetically heterogeneous rats with mitochondrial genomes from either the BN (OKC-HETB, a.k.a “B” genotype) or WKY (OKC-HETW a.k.a “W” genotype) parental strains. These two mitochondrial genomes differ at 94 nucleotides, more akin to human mitochondrial genome diversity than that available in classical laboratory mouse strains. Body weights of the B and W genotypes were similar. However, mitochondrial genotype antagonistically affected grip strength and treadmill endurance in females only. In addition, mitochondrial genotype significantly affected multiple responses to a high-fat diet (HFD) and treatment with 17α-estradiol. Contrary to findings in mice in which males only are affected by 17α-estradiol supplementation, female rats fed a HFD beneficially responded to 17α-estradiol treatment as evidenced by declines in body mass, adiposity, and liver mass. Male rats, by contrast, differed in a mitochondrial genotype-specific manner, with only B males responding to 17α-estradiol treatment. Mitochondrial genotype and sex differences were also observed in features of brain-specific antioxidant response to a HFD and 17α-estradiol as shown by hippocampal levels of Sod2 acetylation, JNK, and FoxO3a. These results emphasize the importance of mitochondrial genotype in assessing responses to putative interventions in aging processes.
CRISPR/Cas9-mediated SNAC9 mutants reveal the positive regulation of tomato ripening by SNAC9 and the mechanism of carotenoid metabolism regulation
Authors: Feng Yuan , Kou Xiaohong , Yuan Shuai , Wu Caie , Zhao Xiaoyang , Xue Zhaohui , Li Qingxiu , Huang Zhengyu , Sun Yijie
Published: February 2023

NAC transcriptional regulators are crucial for tomato ripening. Virus-induced gene silencing (VIGS) of SNAC9 (SlNAC19, Gene ID: 101248665) affects tomato ripening, and SNAC9 is involved in ethylene and abscisic acid (ABA) metabolic pathways. However, the function of SNAC9 in pigment metabolism in tomatoes remains unclear. This work seeks to discover the mechanism of SNAC9 involvement in pigment metabolism during tomato ripening by establishing a SNAC9 knockout model using CRISPR/Cas9 technology. The results indicated that fruit ripening was delayed in knockout (KO) mutants, and SNAC9 mutation significantly affected carotenoid metabolism. The chlorophyll (Chl) degradation rate, total carotenoid content, and lycopene content decreased significantly in the mutants. The transformation rate of chloroplasts to chromoplasts in mutants was slower, which was related to the carotenoid content. Furthermore, SNAC9 changed the expression of critical genes (PSY1, PDS, CRTISO, Z-ISO, SGR1, DXS2, LCYE, LCYB, and CrtR-b2) involved in pigment metabolism in tomato ripening. SNAC9 knockout also altered the expression levels of critical genes involved in the biosynthesis of ethylene and ABA. Accordingly, SNAC9 regulated carotenoid metabolism by directly regulating PSY1, DXS2, SGR1, and CrtR-b2. This research provides a foundation for developing the tomato ripening network and precise tomato ripening regulation.
Field investigation of high reported non-neonatal tetanus burden in Uganda, 2016–2017
Authors: Casey Rebecca Mary , Nguna Joyce , Opar Bernard , Ampaire Immaculate , Lubwama Joseph , Tanifum Patricia , Zhu Bao-Ping , Kisakye Annet , Kabwongera Eva , Tohme Rania A , Dahl Benjamin A , Ridpath Alison D , Scobie Heather M
Published: February 2023

Background

Despite providing tetanus-toxoid-containing vaccine (TTCV) to infants and reproductive-age women, Uganda reports one of the highest incidences of non-neonatal tetanus (non-NT). Prompted by unusual epidemiologic trends among reported non-NT cases, we conducted a retrospective record review to see whether these data reflected true disease burden.

Methods

We analysed nationally reported non-NT cases during 2012–2017. We visited 26 facilities (14 hospitals, 12 health centres) reporting high numbers of non-NT cases (n = 20) or zero cases (n = 6). We identified non-NT cases in facility registers during 1 January 2016–30 June 2017; the identified case records were abstracted.

Results

During 2012–2017, a total of 24 518 non-NT cases were reported and 74% were ≥5 years old. The average annual incidence was 3.43 per 100 000 population based on inpatient admissions. Among 482 non-NT inpatient cases reported during 1 January 2016–30 June 2017 from hospitals visited, 342 (71%) were identified in facility registers, despite missing register data (21%). Males comprised 283 (83%) of identified cases and 60% were ≥15 years old. Of 145 cases with detailed records, 134 (92%) were clinically confirmed tetanus; among these, the case-fatality ratio (CFR) was 54%. Fourteen cases were identified at two hospitals reporting zero cases. Among >4000 outpatient cases reported from health centres visited, only 3 cases were identified; the remainder were data errors.

Conclusions

A substantial number of non-NT cases and deaths occur in Uganda. The high CFR and high non-NT burden among men and older children indicate the need for TTCV booster doses across the life course to all individuals as well as improved coverage with the TTCV primary series. The observed data errors indicate the need for data quality improvement activities.
The Fundamental Fiber Sequence in Étale Homotopy Theory
Authors: Haine Peter J , Holzschuh Tim , Wolf Sebastian
Published: February 2023

Let $ k $ be a field with separable closure $ \bar {k} \supset k $, and let $ X $ be a qcqs $ k $-scheme. We use the theory of profinite Galois categories developed by Barwick–Glasman–Haine to provide a quick conceptual proof that the sequences $ \Pi _{<\infty }^{\'{e}\textrm {t}}(X_{\bar {k}}) \to \Pi _{<\infty }^{\'{e}\textrm {t}}(X) \to \text {BGal}(\bar {k}/k) $ and $ \widehat {\Pi }_{\infty }^{\'{e}\textrm {t}}(X_{\bar {k}}) \to \widehat {\Pi }_{\infty }^{\'{e}\textrm {t}}(X) \to \text {BGal}(\bar {k}/k) $ of protruncated and profinite étale homotopy types are fiber sequences. This gives a common conceptual reason for the following two phenomena: first, the higher étale homotopy groups of $ X $ and the geometric fiber $ X_{\bar {k}} $ are isomorphic, and second, if $ X_{\bar {k}} $ is connected, then the sequence of profinite étale fundamental groups $ 1 \to \hat {\pi }^{\'{e}\textrm {t}}_1(X_{\bar {k}}) \to \hat {\pi }^{\'{e}\textrm {t}}_1(X) \to \text {Gal}(\bar {k}/k) \to 1 $ is exact. It also proves the analogous results for the groupe fondamental élargi of SGA3.
LDH and the MELD-LDH in Severe Acute Liver Injury and Acute Liver Failure: Preliminary Confirmation of a Novel Prognostic Score for Risk Stratification
Authors: Price Jake R , Hagrass Hoda , Filip Ari B , McGill Mitchell R
Published: February 2023

Background

Acute liver failure (ALF) is a devastating condition with high mortality. Currently, liver transplantation is the only life-saving treatment, but the decision to transplant is difficult due to the rapid progression of ALF and persistent shortage of donor organs. Biomarkers that predict death better than current prognostics could help. To our surprise, proteomics recently revealed that lactate dehydrogenase (LDH) is prognostic in ALF by itself and in a novel form of the model for end-stage liver disease (MELD) score called the MELD-LDH. The purpose of this study was to confirm our proteomics results in a larger population.

Methods

We reviewed laboratory data from 238 patients admitted to the University of Arkansas for Medical Sciences Medical Center with a diagnosis of ALF and biochemical evidence of acute liver failure over a 12-year period, as well as subset of 170 patients with encephalopathy.

Results

LDH was strikingly elevated in the nonsurvivors at the time of peak injury. Receiver operating characteristic (ROC) curve analyses revealed that LDH by itself could discriminate between survivors and nonsurvivors on the first day of hospitalization, although not as well as the MELD and MELD-LDH scores that performed alike. Importantly, however, LDH by itself performed similarly to the MELD at the time of peak injury and the MELD-LDH score moderately outperformed both. The MELD-LDH score also had greater sensitivity and negative predictive value than the MELD and the King’s College Criteria.

Conclusions

The results support our prior finding that LDH and the MELD-LDH score predict death and therefore transplant need in ALF patients.
Insights on the evolution and conservation of Appalachian burrowing crayfishes, with the description of a new species ofCambarusErichson, 1846 (Decapoda: Astacidea: Cambaridae)
Authors: Thoma Roger , Hurt Carla , Williams Carl , Withers David
Published: February 2023

A new species of crayfish, Cambarus nyxn. sp., is described from the Kentucky/Tennessee border in the Dissected Appalachian Plateau sub-ecoregion of the US. Of the recognized species of Cambarus Erichson, 1846, it is morphologically most similar to Cambarus deweesae Bouchard & Etnier, 1979, found primarily in the Southern Limestone/Dolomite Valleys and Low Rolling Hills sub-ecoregion. Cambarus nyxn. sp., is distinguishable from other recognized congeners, except for C. deweesae, by the strongly serrated lateral margin of the propodi of the chelae, closed areola, two rows of palmar tubercles, truncate rostrum with convergent margins, and Form I male (MI) gonopod having a central projection shorter than the mesial process. The new species differs from C. deweesae in coloration (blue vs. red, respectively) and size at maturity only. There is considerable genetic, morphometric, and color variation among populations herein considered as members of the new species. The species has a limited range and highlights once more the need for increased conservation efforts for North American crayfishes. Genetic analysis of C. nyxn. sp. sheds light on the evolutionary process occurring in the crayfishes of the Appalachian Mountains after the origin of Cambarus.
Building the Inter-American Convention against Racism: between Antiracist Pride and Racism Denial
Authors: Xavier Pinto Coelho Luana
Published: February 2023

This article examines the main controversies throughout the negotiation of a regional binding instrument to fight racism that led to the approval of the ‘Inter-American Convention against Racism, Racial Discrimination, and Related Forms of Intolerance’ in 2013. In order to identify the regimes of racism denial that shaped the process, the article explores the major controversies in terms of language, concepts, and the need for a more targeted binding treaty on racism, focusing on the leading role of Brazil. The analysis considers the links between scales; from the regional debate to States’ national discourse and practices, within the context of global efforts to advance standards to fight racism, particularly those established at the third World Conference against Racism, Racial Discrimination, in Durban. By reviewing country reports, drafts of the convention, and analysing interviews with some participants of the debates at the Organization of the American States (OAS), this study assesses how the different strategies deployed served to perpetuate regimes of denial of racism, strongly present in the official discourse and challenged in the building of a binding instrument to fight racism in the Americas. Analysis revealed the deep challenges associated with combating racism as a systemic form of oppression historically linked to the region’s colonial past and legacy of the transatlantic slave trade. Finally, consensus was only reached by moving away from the ‘Durban language’, showing how disputed concepts and remedies highlight that racism remains a politically sensitive issue in the region.
Recent trends of “manels”: gender representation among invited panelists at an international oncology conference
Authors: Kamran Sophia C , Yeap Beow Y , Ghosh Anushka , Aldrighetti Christopher M , Willers Henning , Vapiwala Neha
Published: February 2023

Background

Gender disparities in academic medicine are a long-acknowledged concern, particularly at medical conferences. We investigated gender representation and prevalence of “manels” (all-men panels) among invited speakers at the 2018-2021 American Society of Clinical Oncology Annual Meetings.

Methods

Using American Society of Clinical Oncology online programs, 2018-2021 faculty information was obtained, including perceived or self-reported gender, medical specialty, session type, and topic. Primary outcomes were percentage of manels and proportion of women panelists over time; women representation among specialties and topics were evaluated. Cochran-Armitage and Fisher’s exact tests were used to analyze trends in proportion of manels and women representation over time and to compare each session type, topic, or specialty with other categories combined, respectively.

Results

During 2018-2021, there were 670 sessions, 81 of which (12.1%) were manels. Among 2475 panelists, 1181 (47.7%) were women. Over time, the percentage of manels significantly decreased from 17.4% in 2018 to 9.9% in 2021 (P = .030). The highest proportion of manels was observed for leadership or special sessions (17.1%, P = .419). Women panelists were underrepresented for the topics of genitourinary cancers (38.6%, P = .029) and translational or preclinical sciences (36.7%, P < .001). There was a positive trend toward improved women representation among translational or preclinical sciences (27.4% in 2018 vs 41.8% in 2021, P = .031) but not among genitourinary cancers (41.1% in 2018 vs 40.7% in 2021, P = .969).

Conclusions

The number of women panelists increased during the study period, with a corresponding decrease in the proportion of manels, specifically in education and leadership or special sessions. Ongoing underrepresentation of women in genitourinary cancers and translational or preclinical topics underscores the importance of annual meeting organizers continuing to strive for diverse gender representation.
Hedonic Appetite, Affect, and Loss of Control Eating: Macrotemporal and Microtemporal Associations in Adolescents
Authors: Bejarano Carolina M , Hesse Daryl R , Cushing Christopher C
Published: February 2023

Objective

Loss of control eating (LOC) is a dysregulated eating behavior relevant to eating disorders and weight-related health concerns. Hedonic appetite and affect (positive/negative) are dynamic microtemporal processes that influence LOC, but they have been studied predominantly in a static, macrotemporal manner. The present study examined associations of hedonic appetite and positive/negative affect, on macrotemporal and microtemporal levels, with LOC in adolescents.

Methods

Adolescent participants 13–18 years old (n = 43; Mage = 15.1, SD  = 1.6; 69.8% female) completed smartphone surveys for 6 evenings, assessing LOC, hedonic appetite, and positive/negative affect. Scores on items were calculated to create microtemporal and macrotemporal assessments of these constructs. Multilevel models were run to examine associations between hedonic appetite and positive/negative affect with LOC.

Results

Both macrotemporal and microtemporal hedonic appetite were significantly positively related to LOC (β = .73, p < .001; β = .47, p < .001, respectively). Macrotemporal positive affect was significantly negatively associated with LOC (β = −.09, p < .001). Macrotemporal negative affect was significantly positively associated with LOC (β = .13, p < .001). No significant relationships emerged between microtemporal positive/negative affect and LOC.

Conclusions

Hedonic appetite appears to be associated with LOC on both microtemporal and macrotemporal levels, suggesting that both momentary fluctuations and having higher hedonic appetite than others can be risk factors for LOC. However, affect appears to be associated with LOC only at the macrotemporal level. Findings may inform theoretical work and clinical and research assessment strategies.
The impact ofTP53status of tumor cells including the type and the concentration of administered 10B delivery agents on compound biological effectiveness in boron neutron capture therapy
Authors: Masunaga Shin-ichiro , Sanada Yu , Takata Takushi , Tanaka Hiroki , Sakurai Yoshinori , Suzuki Minoru , Kirihata Mitsunori , Ono Koji
Published: February 2023

Human head and neck squamous cell carcinoma cells transfected with mutant TP53 (SAS/mp53) or neo vector (SAS/neo) were inoculated subcutaneously into left hind legs of nude mice. After the subcutaneous administration of a 10B-carrier, boronophenylalanine-10B (BPA) or sodium mercaptododecaborate-10B (BSH), at two separate concentrations, the 10B concentrations in tumors were measured using γ-ray spectrometry. The tumor-bearing mice received 5-bromo-2’-deoxyuridine (BrdU) continuously to label all intratumor proliferating (P) tumor cells, then were administered with BPA or BSH. Subsequently, the tumors were irradiated with reactor neutron beams during the time of which 10B concentrations were kept at levels similar to each other. Following irradiation, cells from some tumors were isolated and incubated with a cytokinesis blocker. The responses of BrdU-unlabeled quiescent (Q) and total (= P + Q) tumor cells were assessed based on the frequencies of micronucleation using immunofluorescence staining for BrdU. In both SAS/neo and SAS/mp53 tumors, the compound biological effectiveness (CBE) values were higher in Q cells and in the use of BPA than total cells and BSH, respectively. The higher the administered concentrations were, the smaller the CBE values became, with a clearer tendency in SAS/neo tumors and the use of BPA than in SAS/mp53 tumors and BSH, respectively. The values for BPA that delivers into solid tumors more dependently on uptake capacity of tumor cells than BSH became more alterable. Tumor micro-environmental heterogeneity might partially influence on the CBE value. The CBE value can be regarded as one of the indices showing the level of intratumor heterogeneity.
A big ask: Sex and data collection
Authors: Sullivan Alice
Published: February 2023

What is happening with sex-based data collection? Alice Sullivan addresses contemporary confusions and controversies
A nested error regression model with high-dimensional parameter for small area estimation
Authors: Lahiri Partha , Salvati Nicola
Published: February 2023

In this paper, we propose a flexible nested error regression small area model with high-dimensional parameter that incorporates heterogeneity in regression coefficients and variance components. We develop a new robust small area-specific estimating equations method that allows appropriate pooling of a large number of areas in estimating small area-specific model parameters. We propose a parametric bootstrap and jackknife method to estimate not only the mean squared errors but also other commonly used uncertainty measures such as standard errors and coefficients of variation. We conduct both model-based and design-based simulation experiments and real-life data analysis to evaluate the proposed methodology.
Epigenetic and chromosomal features drive transposon insertion inDrosophila melanogaster
Authors: Cao Jichuan , Yu Tianxiong , Xu Bo , Hu Zhongren , Zhang Xiao-ou , Theurkauf William E , Weng Zhiping
Published: February 2023

Transposons are mobile genetic elements prevalent in the genomes of most species. The distribution of transposons within a genome reflects the actions of two opposing processes: initial insertion site selection, and selective pressure from the host. By analyzing whole-genome sequencing data from transposon-activated Drosophila melanogaster, we identified 43 316 de novo and 237 germline insertions from four long-terminal-repeat (LTR) transposons, one LINE transposon (I-element), and one DNA transposon (P-element). We found that all transposon types favored insertion into promoters de novo, but otherwise displayed distinct insertion patterns. De novo and germline P-element insertions preferred replication origins, often landing in a narrow region around transcription start sites and in regions of high chromatin accessibility. De novo LTR transposon insertions preferred regions with high H3K36me3, promoters and exons of active genes; within genes, LTR insertion frequency correlated with gene expression. De novo I-element insertion density increased with distance from the centromere. Germline I-element and LTR transposon insertions were depleted in promoters and exons, suggesting strong selective pressure to remove transposons from functional elements. Transposon movement is associated with genome evolution and disease; therefore, our results can improve our understanding of genome and disease biology.