bluuebunny/crossref_metadata_2025_split huggingface dataset:
Machine learning in marine ecology: an overview of techniques and applications
Authors: Rubbens Peter , Brodie Stephanie , Cordier Tristan , Destro Barcellos Diogo , Devos Paul , Fernandes-Salvador Jose A , Fincham Jennifer I , Gomes Alessandra , Handegard Nils Olav , Howell Kerry , Jamet Cédric , Kartveit Kyrre Heldal , Moustahfid Hassan , Parcerisas Clea , Politikos Dimitris , Sauzède Raphaëlle , Sokolova Maria , Uusitalo Laura , Van den Bulcke Laure , van Helmond Aloysius T M , Watson Jordan T , Welch Heather , Beltran-Perez Oscar , Chaffron Samuel , Greenberg David S , Kühn Bernhard , Kiko Rainer , Lo Madiop , Lopes Rubens M , Möller Klas Ove , Michaels William , Pala Ahmet , Romagnan Jean-Baptiste , Schuchert Pia , Seydi Vahid , Villasante Sebastian , Malde Ketil , Irisson Jean-Olivier 
Published: August 2023

AbstractMachine learning covers a large set of algorithms that can be trained to identify patterns in data. Thanks to the increase in the amount of data and computing power available, it has become pervasive across scientific disciplines. We first highlight why machine learning is needed in marine ecology. Then we provide a quick primer on machine learning techniques and vocabulary. We built a database of ∼1000 publications that implement such techniques to analyse marine ecology data. For various data types (images, optical spectra, acoustics, omics, geolocations, biogeochemical profiles, and satellite imagery), we present a historical perspective on applications that proved influential, can serve as templates for new work, or represent the diversity of approaches. Then, we illustrate how machine learning can be used to better understand ecological systems, by combining various sources of marine data. Through this coverage of the literature, we demonstrate an increase in the proportion of marine ecology studies that use machine learning, the pervasiveness of images as a data source, the dominance of machine learning for classification-type problems, and a shift towards deep learning for all data types. This overview is meant to guide researchers who wish to apply machine learning methods to their marine datasets.
Development of microbial enrichments for simultaneous removal of sulfur and nitrogenous metabolites in saline water aquaculture
Authors: Patil Prasanna Kumar , Nagaraju Vinay Tharabenahalli , Baskaran Viswanathan , Avunje Satheesha , Rameshbabu Rajesh , Ghate Sudeep D , Solanki Haresh G 
Published: August 2023

Abstract

Aim
The aim of the study was to develop microbial enrichments from the nitrifying microbial consortia and the environment for simultaneous removal of ammonia, nitrate, and sulfide in aquaculture systems at varied salinities.

Methods and results
Sulfur and nitrogen metabolites are the major factors affecting the farmed aquatic animal species and deteriorate the receiving environments causing ecological damage. The present study reports the development of microbial enrichments from the nitrifying microbial consortia and the environment. The enrichments used thiosulfate or thiocyanate as an energy source and simultaneously removed sulfur, ammonia, and nitrite in spiked medium (125 mg/l ammonia; 145 mg/l nitrite). Further, the microbes in the enrichments could grow up to 30 g/l salinity. Metagenomic studies revealed limited microbial diversity suggesting the enrichment of highly specialized taxa, and co-occurrence network analysis showed the formation of three micro-niches with multiple interactions at different taxonomic levels.

Conclusions
The ability of the enrichments to grow in both organic and inorganic medium and simultaneous removal of sulfide, ammonia, and nitrite under varied salinities suggests their potential application in sulfur, nitrogen, and organic matter-rich aquaculture pond environments and other industrial effluents.
The value of parental medical records for the prediction of diabetes and cardiovascular disease: a novel method for generating and incorporating family histories
Authors: Barak-Corren Yuval , Tsurel David , Keidar Daphna , Gofer Ilan , Shahaf Dafna , Leventer-Roberts Maya , Barda Noam , Reis Ben Y 
Published: August 2023

Abstract

Objective
To determine whether data-driven family histories (DDFH) derived from linked EHRs of patients and their parents can improve prediction of patients’ 10-year risk of diabetes and atherosclerotic cardiovascular disease (ASCVD).

Materials and Methods
A retrospective cohort study using data from Israel’s largest healthcare organization. A random sample of 200 000 subjects aged 40–60 years on the index date (January 1, 2010) was included. Subjects with insufficient history (&lt;1 year) or insufficient follow-up (&lt;10 years) were excluded. Two separate XGBoost models were developed—1 for diabetes and 1 for ASCVD—to predict the 10-year risk for each outcome based on data available prior to the index date of January 1, 2010.

Results
Overall, the study included 110 734 subject-father-mother triplets. There were 22 153 cases of diabetes (20%) and 11 715 cases of ASCVD (10.6%). The addition of parental information significantly improved prediction of diabetes risk (P &lt; .001), but not ASCVD risk. For both outcomes, maternal medical history was more predictive than paternal medical history. A binary variable summarizing parental disease state delivered similar predictive results to the full parental EHR.

Discussion
The increasing availability of EHRs for multiple family generations makes DDFH possible and can assist in delivering more personalized and precise medicine to patients. Consent frameworks must be established to enable sharing of information across generations, and the results suggest that sharing the full records may not be necessary.

Conclusion
DDFH can address limitations of patient self-reported family history, and it improves clinical predictions for some conditions, but not for all, and particularly among younger adults.
Hippocampal transcriptome analysis reveals mechanisms of cognitive impairment in beagle dogs with type 1 diabetes
Authors: Han Qingyue , Ding Qingyu , Yu Luyao , Li Tingyu , Sun Bingxia , Tang Zhaoxin 
Published: August 2023

Abstract
Diabetic encephalopathy is a common complication of type 1 diabetes. However, there have been few studies on cognitive impairment and hippocampal damage in type 1 diabetes mellitus (T1DM) using dogs as experimental animals. To investigate the effects of diabetes on the CNS, 40 adult beagles were divided into streptozotocin/alloxan type 1 diabetes model and control groups. The duration of diabetes in the model group was 120 days. A cognitive dysfunction scale was used to assess cognitive function. Hematoxylin and eosin and Golgi-Cox staining methods were used to observe morphological damage to the hippocampus. Transcriptomics was used to investigate differential gene expression in the hippocampus. The results showed that the cognitive dysfunction score of the model group was significantly higher than that of the control group. In addition, the number of normal neurons, the complexity of dendritic morphology, and the density of dendritic spines were decreased in the hippocampus of diabetic dogs. A total of 672 differentially expressed genes (DEGs) were identified, 289 of which were upregulated, and 383 were downregulated. Modified genes included DBH, IGFBP2, AVPR1A, and DRAXIN. In conclusion, type 1 diabetic dogs exhibit cognitive dysfunction. The DEGs were mainly enriched in metabolic, PI3K-Akt signaling, and neuroactive ligand-receptor interaction pathways.
Kinematics of Galactic Centre clouds shaped by shear-seeded solenoidal turbulence
Authors: Petkova Maya A , Kruijssen J M Diederik , Henshaw Jonathan D , Longmore Steven N , Glover Simon C O , Sormani Mattia C , Armillotta Lucia , Barnes Ashley T , Klessen Ralf S , Nogueras-Lara Francisco , Tress Robin G , Armijos-Abendaño Jairo , Colzi Laura , Federrath Christoph , García Pablo , Ginsburg Adam , Henkel Christian , Martín Sergio , Riquelme Denise , Rivilla Víctor M 
Published: August 2023

ABSTRACT
The Central Molecular Zone (CMZ; the central ∼500 pc of the Galaxy) is a kinematically unusual environment relative to the Galactic disc, with high-velocity dispersions and a steep size–linewidth relation of the molecular clouds. In addition, the CMZ region has a significantly lower star formation rate (SFR) than expected by its large amount of dense gas. An important factor in explaining the low SFR is the turbulent state of the star-forming gas, which seems to be dominated by rotational modes. However, the turbulence driving mechanism remains unclear. In this work, we investigate how the Galactic gravitational potential affects the turbulence in CMZ clouds. We focus on the CMZ cloud G0.253+0.016 (‘the Brick’), which is very quiescent and unlikely to be kinematically dominated by stellar feedback. We demonstrate that several kinematic properties of the Brick arise naturally in a cloud-scale hydrodynamics simulation, that takes into account the Galactic gravitational potential. These properties include the line-of-sight velocity distribution, the steepened size–linewidth relation, and the predominantly solenoidal nature of the turbulence. Within the simulation, these properties result from the Galactic shear in combination with the cloud’s gravitational collapse. This is a strong indication that the Galactic gravitational potential plays a crucial role in shaping the CMZ gas kinematics, and is a major contributor to suppressing the SFR, by inducing predominantly solenoidal turbulent modes.
Reverberation of pulsar wind nebulae – III. Modelling of the plasma interface empowering a long term radiative evolution
Authors: Bandiera R , Bucciantini N , Olmi B , Torres D F 
Published: August 2023

ABSTRACT
The vast majority of pulsar wind nebulae (PWNe) present in the Galaxy is formed by middle-aged systems characterized by a strong interaction of the PWN itself with the supernova remnant (SNR). Unfortunately, modelling these systems can be quite complex and numerically expensive, due to the non-linearity of the PWN–SNR evolution even in the simple one-dimensional (1D)/one-zone case when the reverse shock of the SNR reaches the PWN, and the two begin to interact (and reverberation starts). Here, we introduce a new numerical technique that couples the numerical efficiency of the one-zone thin shell approach with the reliability of a full ‘Lagrangian’ evolution, able to correctly reproduce the PWN–SNR interaction during the reverberation, and to consistently evolve the particle spectrum beyond. Based on our previous findings, we show that our novel strategy resolves many of the uncertainties present in previous approaches, as the arbitrariness in the SNR structure, and ensure a robust evolution, compatible with results that can be obtained with more complex 1D dynamical approaches. Our approach enable us for the first time to provide reliable spectral models of the later compression phases in the evolution of PWNe. While in general, we found that the compression is less extreme than that obtained without such detailed dynamical considerations, leading to the formation of less structured spectral energy distributions, we still find that a non-negligible fraction of PWNe might experience a super-efficient phase, with the optical and/or X-ray luminosity exceeding the spin-down one.
The effectiveness of adalimumab as an add-on therapy in two cases with leg ulcers in Behçet’s disease resistant to conventional immunosuppressive therapy alone and a review of the literature
Authors: Kaban Nedim , Harman Halil 
Published: August 2023

ABSTRACT
The current report presents two cases with leg ulcers related to Behçet’s disease (BD) resistant to conventional immunosuppressive therapy (CIST) but successfully treated with adalimumab (ADA). BD, which can affect vessels of any size and type, is a systemic vasculitis. In the vascular system, veins are the most predominantly affected blood vessels, with deep vein thrombosis and recurrent superficial vein thrombophlebitis being the most common vascular signs of the disease in the lower extremities. Leg ulcers, commonly associated with vasculitis or deep vein thrombosis, are rare in patients with BD. Conventional immunosuppressive therapy is very critical to prevent relapses and diminish the risk of post-thrombotic syndrome. In patients with BD-associated venous thrombosis (deep vein thrombosis or superficial vein thrombophlebitis) resistant to these treatments, tumour necrosis factor-α inhibitors can be used alone or in combination with traditional disease-modifying antirheumatic drugs. In view of such information, add-on adalimumab treatment was considered appropriate for both patients. Response to this intervention was highly satisfying for the patients at the end of the 6-month treatment. Nonetheless, it warrants further studies directly evaluating the efficacy of tumour necrosis factor-α inhibitors alone in leg ulcers in BD.
Symptom Clusters in Patients With Advanced Cancer: A Prospective Longitudinal Cohort Study to Examine Their Stability and Prognostic Significance
Authors: Simão Diana , Barata Pedro C , Alves Marta , Papoila Ana L , Oliveira Sónia , Lawlor Peter 
Published: August 2023

Abstract
This study’s purpose was to assess symptom cluster (SC) stability during disease progression and determine their strength of association with survival in patients with advanced cancer . Consecutively eligible patients with advanced cancer not receiving cancer-specific treatment and referred to a Tertiary Palliative Care Clinic were enrolled in a prospective cohort study. At first consultation (D0) and in subsequent consultations at day 15 (D15) and day 30 (D30), patients rated 9 symptoms through the Edmonton Symptom Assessment System scale (0-10) and 10 others using a Likert scale (1-5). Principal components factor analysis with varimax rotation was used to determine SCs at each consultation. Of 318 patients with advanced cancer, 301 met eligibility criteria with a median age of 69 years (range 37-94). Three SCs were identified: neuro-psycho-metabolic (NPM), gastrointestinal, and sleep impairment, with some variations in their constitution over time. Exploratory factor analysis accounted for 40% of variance of observed variables in all SCs. Shorter median survival was observed continuously for NPM cluster (D0 23 vs. 58 days, P &lt; .001; D15 41 vs. 104 days, P=.004; D30 46 vs. 114 days, P = .002), although the presence of 2 or more SCs on D0 and D15 also had prognostic significance (D0: 21 vs. 45 days, P = .005; D30: 50 vs. 96 days, P = .040). In a multivariable model, NPM cluster (D0 hazard ratio estimate: HR 1.64; 95%CI, 1.17-2.31; P = .005; D15 HR: 2.51; 95%CI, 1.25-5.05; P = .009; D30 HR: 3.9; 95%CI, 1.54-9.86; P = .004) and hospitalization (D0 HR: 2.27; 95%CI, 1.47-3.51; P &lt; .001; D15 HR: 2.43; 95%CI, 1.18-5.01; P = .016; D30 HR: 3.41; 95%CI, 1.35-8.62; P = .009) were independently and significantly associated with worse survival. Three clinically relevant SCs were identified, and their constitution had small variations, maintaining a stable set of nuclear symptoms through disease progression. Presence of the NPM cluster and hospitalization maintained their prognostic value over time.
Still Soul Searching? Remapping Adolescent Religious Commitment
Authors: Uecker Jeremy E , Bowman Carl Desportes 
Published: August 2023

Abstract
Sociologists know very little about the religious lives of the current generation of American adolescents. This study provides an updated portrait of adolescent religious commitment and direct tests of religious change across cohorts by comparing data from the 2017–2018 National Survey of Moral Formation to the 2002–2003 National Study of Youth and Religion. There has been a significant growth in the percentage of adolescents who are not at all religious (by multiple measures). There has been a less substantial decline in the percentage of adolescents who are highly religious. Changes in religiosity have occurred across sociodemographic groups, though not always at the same rate, resulting in new patterns across gender, race, regional, and socioeconomic lines on some aspects of religiosity. Despite declines in religiosity, however, parental transmission of religion is similar to what it was in the previous generation. The decline in adolescent religiosity, notably, reflects a decline in parental religiosity.
Characteristics and Outcomes of Tracheostomized Patients With and Without COVID-19
Authors: Bahk Jeeyune , Dolan Bridget , Sharma Venus , Sehmbhi Mantej , Fung Jennifer Y , Lee Young Im 
Published: August 2023

IMPORTANCE:
Outcomes of tracheostomized patients with COVID-19 are seldomly investigated with conflicting evidence from the existing literature.

OBJECTIVES:
To create a study evaluating the impact of COVID-19 on tracheostomized patients by comparing clinical outcomes and weaning parameters in COVID-19 positive and negative cohorts.

DESIGN, SETTING, AND PARTICIPANTS:
A retrospective observational cohort study of 604 tracheostomized patients hospitalized in 16 ICUs in New York City between March 9, 2020, and September 8, 2021.

MAIN OUTCOMES AND MEASURES:
Patients were stratified into two cohorts: 398 COVID-19 negative (COVID–ve) and 206 COVID-19 positive (COVID+ve) patients. Clinical characteristics, outcomes, and weaning parameters (first pressure support [PS], tracheostomy collar [TC], speech valve placement, and decannulation) were analyzed.

RESULTS:
COVID+ve had fewer comorbidities including coronary artery disease, congestive heart failure, malignancy, chronic kidney disease, liver disease, and HIV (p < 0.05). Higher Fio
2 (53% vs 44%), positive end-expiratory pressure (PEEP) (7.15 vs 5.69), Pco
2 (45.8 vs 38.2), and lower pH (7.41 vs 7.43) were observed at the time of tracheostomy in COVID+ve (p < 0.005). There was no statistical difference in post-tracheostomy complication rates. Longer time from intubation to tracheostomy (15.90 vs 13.60 d; p = 0.002), tracheostomy to first PS (2.87 vs 1.80 d; p = 0.005), and TC placement (11.07 vs 4.46 d; p < 0.001) were seen in COVID+ve. However, similar time to speech valve placement, decannulation, and significantly lower 1-year mortality (23.3% vs 36.7%; p = 0.001) with higher number of discharges to long-term acute care hospital (LTACH) (23.8% vs 13.6%; p = 0.015) were seen in COVID+ve.

CONCLUSIONS AND RELEVANCE:
Patients with COVID-19 required higher Fio
2 and PEEP ventilatory support at the time of tracheostomy, with no observed change in complication rates. Despite longer initial weaning period with PS or TC, similar time to speech valve placement or decannulation with significantly lower mortality and higher LTACH discharges suggest favorable outcome in COVID-19 positive patients. Higher ventilatory support requirements and prolonged weaning should not be a deterrent to pursuing a tracheostomy.
Prophylactic treatment of lattice degeneration in fellow eyes after repair of uncomplicated primary rhegmatogenous retinal detachment
Authors: Curran Christian D. , Adams Olufemi E. , Vagaggini Tommaso , Sodhi Guneet S. , Prairie Michael L. , Baker Mikayla J. , Sastry Ananth , Ryan Edwin H. , Parke 3r d D. Wilkin. , Mittra Robert A. , Dev Sundeep , Tang Peter H. 
Published: August 2023

Abstract

Purpose:
Evaluate prophylactic treatment (PTx) of lattice degeneration (LD) on retinal tear (RT) and rhegmatogenous retinal detachment (RRD) risk in fellow eyes of patients after primary RRD repair in first eye.

Methods:
This was a consecutive case series with cohort control involving patients with RRD repair from January 1, 2013 through December 31, 2017. Patients received PTx (PTx cohort) or no PTx (No-PTx cohort) in fellow eye with 5 years follow-up. Primary outcome measure was proportion with new fellow eye RT/RRD. Secondary outcomes included logarithm of minimum angle of resolution (logMAR) best-corrected visual acuity (BCVA) and status of myopia, posterior vitreous detachment (PVD), and pseudophakia.

Results:
498 patients were divided into 146 and 352 in PTx and No-PTx cohorts, respectively. PTx cohort developed significantly (P < 0.05) fewer RT/RRD (17%) than No-PTx cohort (41%). PTx significantly (P < 0.05) lowered RT/RRD irrespective of PVD and myopia status. PTx patients undergoing phacoemulsification demonstrated significantly (P < 0.05) less RT/RRD (22%) than No-PTx cohort (31%). There was no significant (P = 0.96) final BCVA difference between PTx (median = 0 logMAR) and No-PTx cohorts (median = 0 logMAR).

Conclusions:
PTx of asymptomatic fellow eye LD reduced RT/RRD risk.
Examining the Connection Between Health Outcomes, State Political Ideology, and Food Access in the United States
Authors: Samudra Rhucha P. , Heboyan Vahé 
Published: August 2023

Objectives:
To estimate the impact of county-level income, access to food, availability of health resources, socioeconomic factors, and state political ideology on population obesity and mental health in US counties.

Design:
We compiled a county-level data set from the US Census, County Health Rankings, USDA Food Environment Atlas, the American Community Survey, and the State Ideology Database. We specify 2 multivariable regression models for county-level obesity rate and per capita poor mental health days and control for rurality, food access, income, availability of health care resources, state political ideology, and socioeconomic characteristics.

Results:
We find that higher food access reduces obesity in counties; an increase in per capita full-service restaurants by 1 unit is associated with reduction in obesity rate by 1.24 points and an increase in per capita grocery stores reduces poor mental health days by 0.14. We also find that counties in liberal-leaning states tend to have lower obesity rates. Access to primary care providers (increase in primary care physicians by 1 is associated with decline in obesity rate by 1.18 points and poor mental health days by 0.11 days), and recreational facilities (increase in recreational facilities per 1000 by 1 is associated with reduction in obesity rate by 3.16 points and poor mental health days by 0.47 days) reduces obesity rates and poor mental health days. Median income is associated with decrease in obesity rate and poor mental health days. Increase in median household income by 1% is associated with reduction in obesity rate 4.75% and reduction in poor mental health days by 1.39 days.

Conclusions:
We find that access to food and health care at county level and state ideology through policy making affects health outcomes. Our analysis indicates that counties can improve access to food and health care by investing in these services thereby improving county-level health outcomes and save dollars in the process.