bluuebunny/crossref_metadata_2025_split huggingface dataset:
Structural, magnetic and antibacterial studies of gadolinium doped cobalt ferrite nanoparticles synthesized at low temperature
Authors: Anitha Reddy R , Venkateswara Rao A , Rajesh Babu B , Rama Rao K , Raghavendra V 
Published: March 2023

Abstract
In this work structural, magnetic and antimicrobial studies of gadolinium (Gd) doped cobalt ferrite nanopowder samples were synthesised through facile auto-combustion route using citric acid as combustion agent. The pristine nanopowders were sintered at 600 °C. X-ray diffraction (XRD), infrared spectroscopy (IR) measurements indicated the formation of a single spinel phase. The lattice constant gradually increased from 8.3801 Å to 8.3915 Å with increasing Gd concentration. The average crystallite size varied from 54 nm to 42.7 nm. The correlation between the cation distribution from XRD and the magnetic properties is discussed. The substitution of Gd ions significantly reduced the magnetisation from 60.6 to 36.6 emu g−1 and increased the coercivity. Antimicrobial activities of pure and Gd substituted cobalt ferrite are carried out against Gram-positive (Bacillus subtilis) and Gram-negative (Escherichia coli, Pseudomonas aeruginosa) and also against fungi strain (Aspergillus niger) pathogens, suggesting that Gd substitution significantly improves the activity of cobalt ferrite nanopowders.
Adsorption kinetics, isotherm and thermodynamics studies for the removal of cationic dyes from environmental wastewater by reduced graphene oxide adsorbent synthesized via greener way
Authors: Bairy Bapan , Das Piu , Tantubay Kartik , Baskey (Sen) Moni 
Published: March 2023

AbstractSynthetic dyes emerging from wastewater effluents result in a hazardous environment to our society, hence removal of these dye molecules from the water bodies is necessary due to their toxic nature for living beings. In our study, a straightforward one pot synthetic process is conducted to synthesize reduced graphene oxide (RGO) usingAverrhoa carambolafruit extract. To confirm the formation of RGO, different characterization techniques such as Fourier transform infrared spectroscopy (FTIR), UV–Vis spectroscopy and X-Ray Diffraction (XRD) are investigated. Transmission electron microscopy (TEM) and scanning electron microscopy (SEM) are used to understand the morphology of RGO. Adsorption kinetics for pseudo-first order and pseudo-second order has been carried out for both dyes. Freundlich and Langmuir adsorption isotherm models were confirmed to describe each of the adsorption ability responses with high correlation coefficients. Maximum adsorption capacities of methylene blue (MB) and crystal violet (CV) on RGO were 52.308 mg g−1and 31.466 mg g−1respectively. The adsorption ability of this adsorbent is monitored by recyclability in five subsequent cycles and it is observed that up to 5 cycles, there is no significant decrease in adsorption capability. The present study showed that RGO is highly efficient in removing MB and CV dyes from environmental water bodies. The thermodynamics study for the adsorption phenomena of MB and CV dyes on RGO sheet has been investigated.
Investigation of radiomics and deep convolutional neural networks approaches for glioma grading
Authors: Aouadi Souha , Torfeh Tarraf , Arunachalam Yoganathan , Paloor Satheesh , Riyas Mohamed , Hammoud Rabih , Al-Hammadi Noora 
Published: March 2023

Abstract

Purpose. To determine glioma grading by applying radiomic analysis or deep convolutional neural networks (DCNN) and to benchmark both approaches on broader validation sets. Methods. Seven public datasets were considered: (1) low-grade glioma or high-grade glioma (369 patients, BraTS’20) (2) well-differentiated liposarcoma or lipoma (115, LIPO); (3) desmoid-type fibromatosis or extremity soft-tissue sarcomas (203, Desmoid); (4) primary solid liver tumors, either malignant or benign (186, LIVER); (5) gastrointestinal stromal tumors (GISTs) or intra-abdominal gastrointestinal tumors radiologically resembling GISTs (246, GIST); (6) colorectal liver metastases (77, CRLM); and (7) lung metastases of metastatic melanoma (103, Melanoma). Radiomic analysis was performed on 464 (2016) radiomic features for the BraTS’20 (others) datasets respectively. Random forests (RF), Extreme Gradient Boosting (XGBOOST) and a voting algorithm comprising both classifiers were tested. The parameters of the classifiers were optimized using a repeated nested stratified cross-validation process. The feature importance of each classifier was computed using the Gini index or permutation feature importance. DCNN was performed on 2D axial and sagittal slices encompassing the tumor. A balanced database was created, when necessary, using smart slices selection. ResNet50, Xception, EficientNetB0, and EfficientNetB3 were transferred from the ImageNet application to the tumor classification and were fine-tuned. Five-fold stratified cross-validation was performed to evaluate the models. The classification performance of the models was measured using multiple indices including area under the receiver operating characteristic curve (AUC). Results. The best radiomic approach was based on XGBOOST for all datasets; AUC was 0.934 (BraTS’20), 0.86 (LIPO), 0.73 (LIVER), (0.844) Desmoid, 0.76 (GIST), 0.664 (CRLM), and 0.577 (Melanoma) respectively. The best DCNN was based on EfficientNetB0; AUC was 0.99 (BraTS’20), 0.982 (LIPO), 0.977 (LIVER), (0.961) Desmoid, 0.926 (GIST), 0.901 (CRLM), and 0.89 (Melanoma) respectively. Conclusion. Tumor classification can be accurately determined by adapting state-of-the-art machine learning algorithms to the medical context.
StonPy: a tool to parse and query collections of SBGN maps in a graph database
Authors: Rougny Adrien , Balaur Irina , Luna Augustin , Mazein Alexander 
Published: March 2023

AbstractSummaryThe systems biology graphical notation (SBGN) has become the de facto standard for the graphical representation of molecular maps. Having rapid and easy access to the content of large collections of maps is necessary to perform semantic or graph-based analysis of these resources. To this end, we propose StonPy, a new tool to store and query SBGN maps in a Neo4j graph database. StonPy notably includes a data model that takes into account all three SBGN languages and a completion module to automatically build valid SBGN maps from query results. StonPy is built as a library that can be integrated into other software and offers a command-line interface that allows users to easily perform all operations.Availability and implementationStonPy is implemented in Python 3 under a GPLv3 license. Its code and complete documentation are freely available from https://github.com/adrienrougny/stonpy.Supplementary informationSupplementary data are available at Bioinformatics online.
SLEMM: million-scale genomic predictions with window-based SNP weighting
Authors: Cheng Jian , Maltecca Christian , VanRaden Paul M , O'Connell Jeffrey R , Ma Li , Jiang Jicai 
Published: March 2023

Abstract

Motivation
The amount of genomic data is increasing exponentially. Using many genotyped and phenotyped individuals for genomic prediction is appealing yet challenging.

Results
We present SLEMM (short for Stochastic-Lanczos-Expedited Mixed Models), a new software tool, to address the computational challenge. SLEMM builds on an efficient implementation of the stochastic Lanczos algorithm for REML in a framework of mixed models. We further implement SNP weighting in SLEMM to improve its predictions. Extensive analyses on seven public datasets, covering 19 polygenic traits in three plant and three livestock species, showed that SLEMM with SNP weighting had overall the best predictive ability among a variety of genomic prediction methods including GCTA’s empirical BLUP, BayesR, KAML, and LDAK’s BOLT and BayesR models. We also compared the methods using nine dairy traits of ∼300k genotyped cows. All had overall similar prediction accuracies, except that KAML failed to process the data. Additional simulation analyses on up to 3 million individuals and 1 million SNPs showed that SLEMM was advantageous over counterparts as for computational performance. Overall, SLEMM can do million-scale genomic predictions with an accuracy comparable to BayesR.

Availability and implementation
The software is available at https://github.com/jiang18/slemm.
Recruitment-driven fish production in two regions where fish biomass has drastically declined
Authors: Liang Cui , Pauly Daniel , Christensen Villy , Xian Weiwei , Walters Carl 
Published: March 2023

Abstract
Catches have remained relatively high in the Gulf of Thailand and the Bohai Sea, China, despite severe biomass declines (around 95%) evidenced by fishery-independent surveys. Such high production at very low stock sizes is not predicted by simple-surplus production theory, but can be explained by age-structured models that predict high recruitment rates even when biomass per recruit (BPR) has been drastically reduced. Recruitment rates can be reconstructed by estimating changes over time in biomass and BPR, for alternative assumptions about survey catchability, growth, and mortality rates. These reconstructions indicate that likely severe decreases in BPR, due to high fishing mortality rates, imply that total recruitment rates have likely been relatively stable over time, with catch consisting largely of new recruits making up most of the low biomass. These considerations may apply to numerous areas in east and southeast Asia where most of the catch of coastal trawlers is used to produce animal feeds, notably for aquaculture.
Investigating Technology Concepts to Support Rohingya Refugees in Malaysia
Authors: Georgiou Theodoros , Baillie Lynne , Netto Gina , Paterson Sean 
Published: March 2023

Abstract
The Rohingya ethnic group is one of the most persecuted minorities, whose specific circumstances pose unique and interesting challenges. The digital revolution is transforming the world and is leaving refugees behind (UNHCR). In this paper, we present a multiphase user centred approach we used to explore how Rohingya refugees could access assistance by utilizing technology they already have or share; both early on and long after they arrived in a new country. The findings we present from phase 1, which was an early participatory design phase, were confirmed and endorsed by the Rohingya community, UNHCR and local charities during phase 3. These findings, suggest that concepts aiming to assist Rohingya refugees should primarily focus on: safety, social capital, upskilling, and language translation. Finally, we present the iterative user centred design, implementation, and evaluation of one of these concepts focusing on safety, before being deployed within the Rohingya community in Malaysia.
In utero exposure to antiemetic and risk of adult-onset colorectal cancer
Authors: Murphy Caitlin C , Cirillo Piera M , Krigbaum Nickilou Y , Singal Amit G , Cohn Barbara A 
Published: March 2023

AbstractBackgroundIncidence rates of colorectal cancer (CRC) are increasing among adults born in and after the 1960s, implicating pregnancy-related exposures introduced at that time as risk factors. Dicyclomine, an antispasmodic used to treat irritable bowel syndrome, was initially included in Bendectin (comprising doxylamine, pyridoxine, and dicyclomine), an antiemetic prescribed during pregnancy in the 1960s.MethodsWe estimated the association between in utero exposure to Bendectin and risk of CRC in offspring of the Child Health and Development Studies, a multigenerational cohort that enrolled pregnant women in Oakland, CA, between 1959 and 1966 (n = 14 507 mothers and 18 751 liveborn offspring). We reviewed prescribed medications from mothers’ medical records to identify those who received Bendectin during pregnancy. Diagnoses of CRC in adult (aged ≥18 years) offspring were ascertained by linkage with the California Cancer Registry. Cox proportional hazards models were used to estimate adjusted hazard ratios, with follow-up accrued from birth through cancer diagnosis, death, or last contact.ResultsApproximately 5% of offspring (n = 1014) were exposed in utero to Bendectin. Risk of CRC was higher in offspring exposed in utero (adjusted hazard ratio = 3.38, 95% confidence interval [CI] = 1.69 to 6.77) compared with unexposed offspring. Incidence rates of CRC were 30.8 (95% CI = 15.9 to 53.7) and 10.1 (95% CI = 7.9 to 12.8) per 100 000 in offspring exposed to Bendectin and unexposed, respectively.ConclusionsHigher risk of CRC in offspring exposed in utero may be driven by dicyclomine contained in the 3-part formulation of Bendectin used during the 1960s. Experimental studies are needed to clarify these findings and identify mechanisms of risk.
Adolescent immigrant youth: Creating spaces of belonging
Authors: Rodriguez Liliana V 
Published: March 2023

AbstractDrawing on 24 months of participant observation and interviews with adolescent arrivals in the central coast region of California, this study examines how recently arrived immigrant teens create spaces of belonging. This immigrant population is simultaneously undergoing two life-changing transitions—adolescence and immigration. These two, life-altering transitions, greatly shape the trajectories of immigrant youth in the host country. Unfamiliar with US customs, the educational system, or the mainstream language, adolescent arrivals constantly struggle to belong in a place they hardly know. I advance the concept of immigrant youth vitality to conceptually analyze how shared experiences based on the age of migration and context of reception shape how immigrant youth create safe spaces for themselves. As recent immigrants and teenage newcomers, adolescent arrivals are experiencing for the first time the wrath of anti-immigrant politics directed at them. This study shows that adolescent arrivals often navigate life in the host country by relying on the familiar and their collective experiences including discrimination and exclusion to create spaces where they feel safe and welcomed. I find that by claiming safe spaces the youth actively engage in redefining what belonging means, looks, and feels like for newcomer teenagers.
Precarious Legal Patchworking: Detained Immigrants’ Access to Justice
Authors: Martinez-Aranda Mirian G 
Published: March 2023

Abstract
As immigration enforcement increases, so does the detention of immigrants facing the threat of deportation. Detained without the support of a public defender system—a feature of U.S. immigration law—immigrants face a complex immigration court that is adversarial and can produce dire consequences, including family and community exile, violence, or even death, if they are deported. This paper chronicles the experiences of formerly detained immigrants and how they sought to access justice through multiple means while detained. To win their freedom from detention, they engaged in “precarious legal patchworking” (PLP), during which they haphazardly cobbled together legal resources and assistance from multiple sources, including pro-bono aid, Jailhouse Lawyers, and social networks. PLP speaks to the person’s tenacity amidst precarity, but it also unveils the fragility of this strategy because patchworking can extend detention or complicate one’s case. The lack of access to counsel is a form of legal violence, and stratifying access to representation in this way creates an underclass of people who are systematically denied justice.
Association of a variant upstream of growth differentiation factor 11 (GDF11) on carcass traits in crossbred beef cattle
Authors: Spencer Rachel J , Ketel Crystal R , Penner Gregory B , Asai-Coakwell Mika 
Published: March 2023

Abstract
The mature peptide of growth differentiation factor 11 (GDF11) in Bos taurus breeds, shares 90% amino acid sequence similarity to myostatin (MSTN), where loss-of-function mutations result in muscular hyperplasia causing a phenotype known as double-muscling. Mutations in the MSTN coding sequence increase muscle mass and reduce fat and bone tissues, but also confer poor fertility, reduced stress tolerance, and increased calf mortality. GDF11 influences skeletal muscle development in mice, and muscular atrophy can be induced by exogenous GDF11 treatment. To date, there are no reports of GDF11’s role in bovine carcass traits. To determine associations between GDF11 and carcass quality in beef cattle, bovine GDF11 was examined in crossbred Canadian beef cattle populations during finishing. Few coding variants were found in this functionally important gene, but an upstream variant c.1-1951C &gt; T (rs136619751) with a minor allele frequency of 0.31 was identified and further genotyped in two separate populations of crossbred steers (n = 415 and 450). CC animals had lower backfat thickness, marbling percentage, and yield score than CT or TT animals (P &lt; 0.001 and &lt; 0.05). These data suggest a role of GDF11 in carcass quality in beef cattle and may provide a selection tool to improve carcass traits in cattle.
Predictability of the vault after implantable collamer lens implantation using OCT and artificial intelligence in White patient eyes
Authors: Russo Andrea , Filini Ottavia , Savini Giacomo , Festa Giulia , Morescalchi Francesco , Boldini Alessandro , Semeraro Francesco 
Published: March 2023

Purpose:
To compare the predicted vault using machine learning with the achieved vault using the online manufacturer's nomogram in patients undergoing posterior chamber implantation with an implantable collamer lens (ICL).

Setting:
Centro Oculistico Bresciano, Brescia, Italy, and I.R.C.C.S.—Bietti Foundation, Rome, Italy.

Design:
Retrospective multicenter comparison study.

Methods:
561 eyes from 300 consecutive patients who underwent ICL placement surgery were included in this study. All preoperative and postoperative measurements were obtained by anterior segment optical coherence tomography (AS-OCT; MS-39). The actual vault was quantitatively measured and compared with the predicted vault using machine learning of AS-OCT metrics.

Results:
A strong correlation between model predictions and achieved vaulting was detected by random forest regression (RF; R
2 = 0.36), extra tree regression (ET; R
2 = 0.50), and extreme gradient boosting regression (R
2 = 0.39). Conversely, a high residual difference was observed between achieved vaulting values and those predicted by the multilinear regression (R
2 = 0.33) and ridge regression (R
2 = 0.33). ET and RF regressions showed significantly lower mean absolute errors and higher percentages of eyes within ±250 μm of the intended ICL vault compared with the conventional nomogram (94%, 90%, and 72%, respectively; P < .001). ET classifiers achieved an accuracy (percentage of vault in the range of 250 to 750 μm) of up to 98%.

Conclusions:
Machine learning of preoperative AS-OCT metrics achieved excellent predictability of ICL vault and size, which was significantly higher than the accuracy of the online manufacturer's nomogram, providing the surgeon with a valuable aid for predicting the ICL vault.
Long-term results of hyperopic ablations using alcohol-assisted PRK and FS-LASIK: comparative study
Authors: Asroui Lara , Arba-Mosquera Samuel , Torbey Julien , Ahmed Mohamad A. , Fattah Maamoun A. , Koaik Mona , Awwad Shady T. 
Published: March 2023

Purpose:
To evaluate the long-term visual and refractive outcomes of hyperopic excimer ablation using alcohol-assisted photorefractive keratectomy (PRK) and femtosecond laser–assisted laser in situ keratomileusis (FS-LASIK).

Setting:
American University of Beirut Medical Center, Beirut, Lebanon.

Design:
Retrospective, matched comparative study.

Methods:
Eyes that underwent alcohol-assisted PRK were compared to matched eyes that underwent FS-LASIK. All patients were followed up for at least 3 years after surgery. The refractive and visual outcomes of each group were compared at different postoperative time points. The main outcome measures were spherical equivalent deviation from target (SEDT), manifest refraction, and visual acuity.

Results:
83 eyes underwent alcohol-assisted PRK and 83 matched eyes underwent FS-LASIK. Preoperative manifest refraction spherical equivalent was 2.44 ± 1.18 diopters (D) and 2.20 ± 0.87 D (P = .133) in the PRK and FS-LASIK groups, respectively. Preoperative manifest cylinder was −0.77 ± 0.89 D and −0.61 ± 0.59 D (P = .175) for the PRK and LASIK groups, respectively. 3 years postoperatively, SEDT was 0.28 ± 0.66 D and 0.40 ± 0.56 D for the PRK and LASIK groups, respectively (P = .222), whereas manifest cylinder was −0.55 ± 0.49 D and −0.30 ± 0.34 D for PRK and LASIK, respectively (P < .001). The mean difference vector was 0.59 ± 0.46 for PRK and 0.38 ± 0.32 for LASIK (P < .001). 13.3% of PRK eyes and 0% of LASIK eyes had >1 D of manifest cylinder (P = .003).

Conclusions:
Both alcohol-assisted PRK and FS-LASIK are safe and effective for the treatment of hyperopia. PRK induces slightly more postoperative astigmatism than LASIK. Larger optical zones and recently introduced ablation profiles that lead to a smoother ablation surface might improve the clinical results of hyperopic PRK.
Cigarette smoking, opioid consumption, and pain intensity after major surgery: An observational study
Authors: Wang Yi-Chien , Wang Chien-Wun , Wu Hsiang-Ling , Cata Juan P. , Huang Shih-Yu , Wu Yu-Ming , Chen Jui-Tai , Cherng Yih-Giun , Tai Ying-Hsuan 
Published: March 2023

Background:
Chronic exposure to nicotine may change pain perception and promote opioid intake. This study aimed to evaluate the putative effect of cigarette smoking on opioid requirements and pain intensity after surgery.

Methods:
Patients who underwent major surgery and received intravenous patient-controlled analgesia (IV-PCA) at a medical center between January 2020 and March 2022 were enrolled. Patients’ preoperative smoking status was assessed using a questionnaire by certified nurse anesthetists. The primary outcome was postoperative opioid consumption within 3 days after surgery. The secondary outcome was the mean daily maximum pain score, assessed using a self-report 11-point numeric rating scale, and the number of IV-PCA infusion requests within three postoperative days. Multivariable linear regression models were used to calculate the regression coefficient (beta) and 95% confidence interval (CI) for the association between smoking status and outcomes of interest.

Results:
A total of 1162 consecutive patients were categorized into never smokers (n = 968), former smokers (n = 45), and current smokers (n = 149). Current smoking was significantly associated with greater postoperative opioid consumption (beta: 0.296; 95% CI, 0.068-0.523), higher pain scores (beta: 0.087; 95% CI, 0.009-0.166), and more infusion requests (beta: 0.391; 95% CI, 0.073-0.710) compared with never smokers. In a dose-dependent manner, smoking quantity (cigarette per day) was positively correlated with both intraoperative (Spearman’s rho: 0.2207, p = 0.007) and postoperative opioid consumption (Spearman’s rho: 0.1745, p = 0.033) among current smokers.

Conclusion:
Current cigarette smokers experienced higher acute pain, had more IV-PCA infusion requests, and consumed more opioids after surgery. Multimodal analgesia with nonopioid analgesics and opioid-sparing techniques, along with smoking cessation should be considered for this population.