bluuebunny/crossref_metadata_2025_split huggingface dataset:
Enhancing residue degradation and methane production from active sludge: the role of conductive nanoparticles in anaerobic digestion systems
Authors: Alrawashdeh Khalideh Al bkoor , Al-Tabbal Jalal A , AL-Samrraie La’aly A , Al Bsoul Abeer , Al Zboon Kamel K 
Published: January 2024

Abstract
The effects of stepwise addition of conductive nanoparticles (n-C, n-Cu2O, n-ZnO and n-Al2O3) on anaerobic digestion (AD) performance, biogas and CH4 generation, and the removal efficiency of organic matter were thoroughly assessed. The addition of n-C and n-Al2O3 improved the removal efficiencies of total solid by 19.12% and 8.87%, volatile solid by 22.54% and 11.15%, total chemical oxygen demand by 13.6% and 6.27%, degradation efficacy by 4.87% and 2.3%, biogas yields by 20.62% and 8.27% and CH4 content by 11.49% and 8.63%, respectively. Contrarily, the addition of n-ZnO and n-Cu2O had a negative impact on AD performance and led to significant drops in the production of biogas of 34.3% and 57.3%, respectively.
Multiplicities and Dimensions in Enveloping Tensor Categories
Authors: Knop Friedrich 
Published: January 2024

Abstract
In a previous paper, semisimple tensor categories were constructed from certain regular Mal’cev categories. In this paper, we calculate the tensor product multiplicities and the categorical dimensions of the simple objects. This yields also the Grothendieck ring. The main tool is the subquotient decomposition of the generating objects.
Clinical Cytogenetics: Current Practices and Beyond
Authors: Mathew Mariam T , Babcock Melanie , Hou Ying-Chen Claire , Hunter Jesse M , Leung Marco L , Mei Hui , Schieffer Kathleen , Akkari Yassmine 
Published: January 2024

Abstract

Background
Throughout history, the field of cytogenetics has witnessed significant changes due to the constant evolution of technologies used to assess chromosome number and structure. Similar to the evolution of single nucleotide variant detection from Sanger sequencing to next-generation sequencing, the identification of chromosome alterations has progressed from banding to fluorescence in situ hybridization (FISH) to chromosomal microarrays. More recently, emerging technologies such as optical genome mapping and genome sequencing have made noteworthy contributions to clinical laboratory testing in the field of cytogenetics.

Content
In this review, we journey through some of the most pivotal discoveries that have shaped the development of clinical cytogenetics testing. We also explore the current test offerings, their uses and limitations, and future directions in technology advancements.

Summary
Cytogenetics methods, including banding and targeted assessments like FISH, continue to hold crucial roles in cytogenetic testing. These methods offer a rapid turnaround time, especially for conditions with a known etiology involving recognized cytogenetic aberrations. Additionally, laboratories have the flexibility to now employ higher-throughput methodologies to enhance resolution for cases with greater complexity.
Clinical Utility and Benefits of Comprehensive Genomic Profiling in Cancer
Authors: Tjota Melissa Yuwono , Segal Jeremy P , Wang Peng 
Published: January 2024

Abstract

Background
Comprehensive genomic profiling (CGP) with next-generation sequencing detects genetic alterations of hundreds of genes simultaneously and multiple molecular biomarkers with one test. In the personalized medicine era, CGP is increasingly used for cancer diagnosis, treatment selection, and prognosis prediction.

Content
In this review, we summarize the benefits of CGP, clinical utility of CGP, and challenges of setting up CGP in the clinical laboratories. Besides the genetic alterations identified in the cancer-related genes, other biomarkers such as tumor mutational burden, microsatellite instability, and homologous recombination deficiency are critical for initiating targeted therapy. Compared with conventional tests, CGP uses less specimen and shortens the turnaround time if multiple biomarkers need to be tested. RNA fusion assay and liquid biopsy are helpful additions to DNA-based CGP by detecting fusions/splicing variants and complementing tissue-based CGP findings, respectively.

Summary
Many previous hurdles for implementing CGP in the clinical laboratories have been gradually alleviated such as the decrease in sequencing cost, availability of both open-source and commercial bioinformatics tools, and improved reimbursement. These changes have helped to make CGP available to a greater population of cancer patients for improving characterization of their tumors and expanding their eligibility for clinical trials. Additionally, sequencing results of the hundreds of genes on CGP panels could be further analyzed to better understand the biology of various cancers and identify new biomarkers.
Cost Effectiveness of Genomic Population Health Screening in Adults: A Review of Modeling Studies and Future Directions
Authors: Wildin Robert S 
Published: January 2024

Abstract

Background
Detecting actionable health risks for genetic diseases prior to symptomatic presentation at population scale using genomic test technologies is a preventive health innovation being piloted in multiple locations. Standard practice is to screen for risks only in those with personal or family history of specific disease. Genomic population heath screening has proven feasible and potentially scalable. The value of this intervention in terms of economic benefit has been scientifically modeled by several groups.

Content
Eight recent cost-effectiveness modeling studies for high penetrance monogenic dominant diseases that used input parameters from 3 different countries are reviewed. Results and their uses in refining implementations are analyzed and the roles for laboratory medicine in facilitating success are discussed.

Summary
The reviewed studies generally found evidence for cost-effectiveness of genomic population health screening in at least a subset of their base case screening scenario. Sensitivity analyses identified opportunities for improving the likelihood of cost-effectiveness. On the whole, the modeling results suggest genomic population health screening is likely to be cost-effective for high penetrance disorders in younger adults, especially with achievable reductions in test cost effected partially through combining tests for individual disorders into one screening procedure. Policies founded on the models studied should consider limitations of the modeling methods and the potential for impacts on equity and access in the design and implementation of genomic screening programs.
Effect of the pelleting process on diet formulations with varying levels of crystalline amino acids and reducing sugars on digestibility in growing pigs
Authors: Dunmire Kara M , Lopez Diego A , Zhang Yiqin , Jones Cassandra K , Li Yonghui , Woodworth Jason C , Goodband Robert D , Tokach Michael D , Stark Charles R , Stein Hans H , Paulk Chad B 
Published: January 2024

Abstract
The objective of this experiment was to determine the effects of pelleting on the standardized ileal digestibility (SID) of amino acids (AA) and crude protein (CP) in diets with or without increased concentrations of free AA and reducing sugars (RS). Eight individually housed, ileal cannulated barrows (initially 31.4 kg) were allotted to an 8 × 8 Latin square with eight diets and eight 7-d periods with ileal digesta collected on days 6 and 7. Treatments were arranged in a 2 × 2 × 2 factorial with the main effects of diet form (mash or pellet), crystalline AA (low or high), or RS (low or high), provided by distillers dried grains with solubles and bakery meal. Diets were pelleted to achieve a hot pellet temperature of 85 to 88 °C. Data were analyzed as a Latin square design using the GLIMMIX procedure of SAS 9.4. A feed form × RS interaction (P &lt; 0.026) for SID of tryptophan was observed. Feeding pelleted low RS diets increased SID of tryptophan compared with mash high and low RS diets, and pelleted high RS diets. For the main effects of feed form, the SID of total AA, CP, and indispensable AA was greater (P &lt; 0.042) in pelleted diets compared with mash diets. For the main effects of crystalline AA, pigs fed high crystalline AA had increased (P = 0.007) SID of tryptophan and decreased (P = 0.050) SID of histidine compared with those fed low crystalline AA diets. For the main effects of RS, high RS diets had decreased (P &lt; 0.05) SID of total AA, CP, and indispensable AA compared with low RS diets. In conclusion, pelleting diets increased AA digestibility, and pelleting diets with increased crystalline AA or RS did not affect the improvement in AA digestibility from pelleting. Diets formulated with high crystalline AA had increased SID of tryptophan. Formulating diets with high RS resulted in decreased AA digestibility compared with corn–soybean meal-based diets.
Continuity of Radiologists Between Diagnostic Breast Imaging and Image-Guided Breast Biopsy: Impact on Patient-Reported Biopsy Morbidity Experiences
Authors: McLaughlin Carol , Moorman Sarah E H , Yin Chen , Shankar Prasad R , Davenport Matthew S , Neal Colleen H , Pinsky Renee W , Pujara Akshat C 
Published: January 2024

Abstract

Objective
To determine whether continuity of care between diagnostic breast imaging and subsequent image-guided breast biopsy could reduce patient-reported biopsy-related morbidity.

Methods
This was a prospective, pragmatically randomized, 2-arm health utilities analysis of 200 women undergoing diagnostic breast imaging followed by US- or stereotactic-guided breast biopsy at a single quaternary care center from September 3, 2019, to April 10, 2023. Breast biopsy–naive women with a BI-RADS 4 or 5 finding at diagnostic imaging were randomly scheduled for the typically first available biopsy appointment. One day after biopsy, enrolled patients were administered the Testing Morbidities Index (TMI). The primary outcome was the difference in TMI summary utility scores in patients who did vs did not have the same radiologist perform diagnostic imaging and biopsy.

Results
Response rates were 63% (100/159) for the different radiologist cohort and 71% (100/140) for the same radiologist cohort; all respondents answered all questions in both arms. Mean time to biopsy was 7 ± 6 days and 10 ± 9 days, and the number of participating radiologists was 11 and 18, respectively. There was no difference in individual measured domains (pain, fear, or anxiety before procedure; pain, embarrassment, fear, or anxiety during procedure; mental or physical impact after procedure; all P &gt;.00625) or in overall patient morbidity (0.83 [95% CI, 0.81–0.85] vs 0.82 [95% CI: 0.80–0.84], P = .66).

Conclusion
Continuity of care between diagnostic breast imaging and image-guided breast biopsy did not affect morbidity associated with breast biopsy, suggesting that patients should be scheduled for the soonest available biopsy appointment rather than waiting for the same radiologist.
Synovium and infrapatellar fat pad share common mesenchymal progenitors and undergo coordinated changes in osteoarthritis
Authors: Li Jun , Gui Tao , Yao Lutian , Guo Hanli , Lin Yu-Lieh , Lu Jiawei , Duffy Michael , Zgonis Miltiadis , Mauck Robert , Dyment Nathaniel , Zhang Yejia , Scanzello Carla , Seale Patrick , Qin Ling 
Published: January 2024

Abstract
Osteoarthritis (OA) affects multiple tissues in the knee joint, including the synovium and intra-articular adipose tissue (IAAT) that are attached to each other. However, whether these two tissues share the same progenitor cells and hence function as a single unit in joint homeostasis and diseases is largely unknown. Single-cell transcriptomic profiling of synovium and infrapatellar fat pad (IFP), the largest IAAT, from control and OA mice revealed five mesenchymal clusters and predicted mesenchymal progenitor cells (MPCs) as the common progenitors for other cells: synovial lining fibroblasts (SLFs), myofibroblasts (MFs), and preadipocytes 1 and 2. Histologic examination of joints in reporter mice having Dpp4-CreER and Prg4-CreER that label MPCs and SLFs, respectively, demonstrated that Dpp4+ MPCs reside in the synovial sublining layer and give rise to Prg4+ SLFs and Perilipin+ adipocytes during growth and OA progression. After OA injury, both MPCs and SLFs gave rise to MFs, which remained in the thickened synovium at later stages of OA. In culture, Dpp4+ MPCs possessed mesenchymal progenitor properties, such as proliferation and multilineage differentiation. In contrast, Prg4+ SLFs did not contribute to adipocytes in IFP and Prg4+ cells barely grew in vitro. Taken together, we demonstrate that the synovium and joint fat pad are one integrated functional tissue sharing common mesenchymal progenitors and undergoing coordinated changes during OA progression.
Genetic susceptibility and late bone outcomes in childhood acute lymphoblastic leukemia survivors
Authors: Nadeau Geneviève , Yazdanpanah Mojgan , Yazdanpanah Nahid , Forgetta Vincenzo , Girard Simon , Sinnett Daniel , Krajinovic Maja , Alos Nathalie , Manousaki Despoina 
Published: January 2024

Abstract
Childhood acute lymphoblastic leukemia (cALL) survivors are at increased risk for bone comorbidities, but accurate screening tools for such comorbidities are limited. Polygenic scores (PGS) could stratify cALL survivors for risk of long–term adverse bone outcomes. We evaluated 214 (51% female) cALL survivors from the Prévenir les Effets TArdifs de la LEucémie study (median age 21 yr). Bone mineral density (BMD) measurements were obtained using dual X–ray absorptiometry at the lumbar spine (LS-BMD), femoral neck (FN-BMD), and total body (TB-BMD), and vertebral fractures (VF) were documented using the vertebral deformity criterion. We computed a PGS for adult heel quantitative ultrasound speed of sound (gSOS), known to be associated with the risk of osteoporotic fracture, using imputed genotype data of the participants, and tested it for association with BMD Z-scores and VF risk, adjusting for clinical risk factors, and in sex and prognostic risk-stratified analyses. We found that a gSOS below the mean was associated with lower BMD in all three sites in univariate and multivariate models. In univariate analyses, 1 SD increase in gSOS conferred a 0.16 SD increase in LS-BMD (95% CI 0.005-0.31), whereas a gSOS above the mean was associated with a 0.31 SD higher LS-BMD (95% CI 0.008-0.61), a 0.36 SD higher TB-BMD (95% CI 0.06-0.67), and a 0.43 SD higher FN-BMD (95% CI 0.13-0.72). Models combining gSOS with clinical risk factors explained up to 16% of the variance of BMD phenotypes and obtained an area under the receiver operating characteristic curve for VF of 0.77 in subgroup analyses. Cranial radiation, high cumulative glucocorticoid doses, high risk group, and male sex were significant risk factors for lower BMD Z-scores. In conclusion, a PGS, in combination with clinical risk factors, could be used as a tool to risk stratify cALL survivors for treatment–related bone morbidity.
Bone loss after discontinuation of denosumab: the devil is in the details
Authors: Minisola Salvatore , Cipriani Cristiana , Colangelo Luciano , Pepe Jessica 
Published: January 2024

Vignette
A 47-year-old postmenopausal woman with osteoporosis was treated with denosumab, which was discontinued due to side effects. She was therefore transitioned to a yearly intravenous infusion of zoledronic acid. An increase in bone turnover markers together with bone loss at the lumbar spine was observed before the second infusion, suggesting an overshooting of bone resorption due to denosumab discontinuation. On physical examination, the patient was restless and reported having lost about 10 kg since the last visit. A solitary left inferior thyroid nodule was noted on neck palpation. Circulating thyroid hormone levels were elevated, with suppressed thyroid-stimulating hormone. A thyroid scan showed increased uptake in the left inferior nodule with suppression of the remainder of the thyroid gland. A diagnosis of hyperthyroidism due to toxic adenoma was made. The patient was treated with radioactive iodine ablation, with consequent complete normalization of thyroid function. She continued yearly treatment with zoledronic acid. She remained clinically well with no further fractures. Bone turnover markers were appropriately suppressed and bone mineral density increased in the spine and hip. This case illustrates how the overshooting phenomenon following denosumab discontinuation may be compounded by the development of secondary conditions, which can result in suboptimal response to antiresorptive osteoporosis medications.
Burosumab vs conventional therapy in children with X-linked hypophosphatemia: results of the open-label, phase 3 extension period
Authors: Ward Leanne M , Högler Wolfgang , Glorieux Francis H , Portale Anthony A , Whyte Michael P , Munns Craig F , Nilsson Ola , Simmons Jill H , Padidela Raja , Namba Noriyuki , Cheong Hae Il , Sochett Etienne , Muroya Koji , Tanaka Hiroyuki , Pitukcheewanont Pisit , Gottesman Gary S , Biggin Andrew , Perwad Farzana , Chen Angel , Lawrence Merritt II John , Imel Erik A 
Published: January 2024

Abstract
In a randomized, open-label phase 3 study of 61 children aged 1–12 years old with X-linked hypophosphatemia (XLH) previously treated with conventional therapy, changing to burosumab every 2 weeks (Q2W) for 64 weeks improved the phosphate metabolism, radiographic rickets, and growth compared with conventional therapy. In this open-label extension period (weeks 64–88), 21 children continued burosumab Q2W at the previous dose or crossed over from conventional therapy to burosumab starting at 0.8 mg/kg Q2W with continued clinical radiographic assessments through week 88. Efficacy endpoints and safety observations were summarized descriptively for both groups (burosumab continuation, n = 6; crossover, n = 15). At week 88 compared with baseline, improvements in the following outcomes were observed in the burosumab continuation and crossover groups, respectively: mean (SD) RGI-C rickets total score (primary outcome), +2.11 (0.27) and +1.89 (0.35); mean (SD) RGI-C lower limb deformity score, +1.61 (0.91) and +0.73 (0.82); and mean (SD) height Z-score + 0.41 (0.50) and +0.08 (0.34). Phosphate metabolism normalized rapidly in the crossover group and persisted in the continuation group. Mean (SD) serum alkaline phosphatase decreased from 169% (43%) of the upper limit of normal (ULN) at baseline to 126% (51%) at week 88 in the continuation group and from 157% (33%) of the ULN at baseline to 111% (23%) at week 88 in the crossover group. During the extension period, treatment-emergent adverse events (AEs) were reported in all 6 children in the burosumab continuation group and 14/15 children in the crossover group. The AE profiles in the randomized and extension periods were similar, with no new safety signals identified. Improvements from baseline in radiographic rickets continued in the extension period among children with XLH who remained on burosumab. Children who crossed over from conventional therapy to burosumab demonstrated a rapid improvement in phosphate metabolism and improved rickets healing over the ensuing 22 weeks.
Comparison of physiological and behavioral nutrition-related factors in people with and without adolescent idiopathic scoliosis, from cohort data at 8 to 20 years
Authors: Ng Phoebe T T , Tucker Kylie , Zahir Syeda Farah , Izatt Maree T , Straker Leon , Claus Andrew 
Published: January 2024

Abstract
Nutrition-related variables including lower body mass index (BMI), lower bone mineral density (BMD), altered body composition and hormone levels have been reported in adolescent idiopathic scoliosis (AIS). The aims of this study were to determine if physiological and behavioral nutrition-related factors differ between people with and without AIS, and to quantify their relationship with AIS, in unbiased cohort sample. BMI, presence of an eating disorder, leptin, adiponectin, BMD, vitamin D, lean mass, and fat mass were compared between those with and without AIS at ages 8, 10, 14, 17, and 20 years, and multiple logistic regression was performed between these variables and AIS. Lower total body BMD (median, 1.0 g/cm2 vs 1.1 g/cm2; p = .03) and lean mass (median, 38.8 kg vs 46.0 kg; p = .04) at age 20 years were observed in those with AIS compared to those without scoliosis. At age 20, the odds of AIS were 3.23 times higher for adolescents with an eating disorder compared to those with no eating disorder (95% CI, 1.02–8.63) when adjusted for BMI. Every 1 kg/m2 increase in BMI decreased the odds of AIS by 0.88 times (95% CI, 0.76–0.98), after adjusting for eating disorder diagnosis. In conclusion, lower BMI in mid-adolescence and presence of eating disorder outcomes, lower BMD, and lower lean mass in late adolescence were associated with the presence of AIS. Current data do not explain the mechanisms for these associations but suggest that serum leptin, adiponectin, and vitamin D are unlikely to be contributing factors. Conclusive determination of the prevalence of eating disorders in AIS will require further studies with larger sample sizes.
The impact of COVID-19 on 2020 monthly incidence trends of primary brain and other CNS tumors
Authors: Cioffi Gino , Waite Kristin A , Price Mackenzie , Neff Corey , Kruchko Carol , Ostrom Quinn T , Barnholtz-Sloan Jill S 
Published: January 2024

Abstract

Background
To mitigate disease spread, restrictions implemented in the United States surrounding the COVID-19 pandemic created an environment that led to delays in cancer diagnosis. The data needed to accurately analyze the impact of the pandemic on brain and CNS tumor incidence has not been available until now. Utilizing incidence data from the Central Brain Tumor Registry of the United States (CBTRUS) we analyzed the impact of the COVID-19 pandemic on primary brain and other CNS tumor incidence for the first year of the pandemic.

Methods
Monthly age-adjusted incidence rates and incidence trends for 2019 and 2020 were determined for age at diagnosis, sex, race, ethnicity, diagnostic confirmation, behavior, tumor histopathology, and county-level urbanization. Monthly incidence rate ratios comparing 2020 and 2019 were evaluated for the same factors.

Results
Overall, there was a notable decrease in incidence rates in March–May 2020 when compared to 2019. These decreases were driven by nonmalignant tumors, with a 50% incidence decrease between March 2020 and 2019. Individuals who were Black had a larger incidence decrease in early 2020 than individuals who were White. Radiographically confirmed tumors saw larger incidence decreases than histologically confirmed tumors. There were no changes in monthly incidence of glioblastoma in 2020 compared to 2019.

Conclusions
These data provide evidence that disruptions in medical care, such as governmental and health care mandates, in response to the COVID-19 pandemic resulted in an overall decreased incidence of primary brain tumors in early 2020.