bluuebunny/crossref_metadata_2025_split huggingface dataset:
Evaluation of post-chemotherapy residual seminomatous masses by 18F-fluorodeoxyglucose PET/CT using tumor-to-liver ratio – conundrum or solution?
Authors: Ghosh Suchismita , Agrawal Archi , Rangarajan Venkatesh , Choudhury Sayak , Maitre Priyamvada , Purandare Nilendu , Shah Sneha , Puranik Ameya , Bakshi Ganesh , Joshi Amit , Prakash Gagan , Menon Santosh , Prabhash Kumar , Norohna Vanita , Pal Mahendra , Murthy Vedang 
Published: September 2023

Objective
Assessment of diagnostic accuracy of FDG-PET/CT in the detection of viable disease in post-chemotherapy seminomatous residual masses using visual interpretation, SUVmax, and T/L ratio.

Methods
This is a retrospective study assessing the post-chemotherapy seminomatous residual masses of size >3 cm. The PET/CT scan findings were interpreted visually for presence of residual disease which were validated from histopathology reports or imaging follow-up for a maximum of 3 years. SUVmax and T/L ratios were also determined for all the residual lesions. Sensitivity, specificity, positive predictive value (PPV), and negative predictive value NPV were calculated and compared for all three parameters along with ROC analysis to obtain an optimal cutoff value for SUVmax and T/L ratio, respectively.

Results
Sample size was 49. Out of these 49 patients, 8 had validation of PET results with histopathology. Rest was validated with imaging follow-up. FDG-PET was positive in 30 patients and negative in 19 patients by visual interpretation. The sensitivity, specificity, PPV, and NPV by this method were 100%, 62.5%, 73%, and 100%, respectively. The SUVmax and T/L ratios were also calculated for these lesions. The cutoff for these two variables was 4.56 and 1.21, respectively. The sensitivity, specificity, PPV, and NPV at these cutoffs were 76%, 87.5%, 86%, 77.7%, and 92%, 87.5%, 88%, 91%, respectively.

Conclusion
FDG-PET has a favorable diagnostic value in predicting viable disease in post-chemotherapy seminomatous residual masses and using T/L ratio cutoff of 1.21 will increase the specificity of the test.
Potential of preoperative fluorodeoxyglucose-positron emission tomography/computed tomography to diagnose contralateral lymph node metastases in patients with oral cancer
Authors: Wamasing Natnicha , Nakamura Shin , Watanabe Hiroshi , Kuribayashi Ami , Miura Masahiko 
Published: September 2023

Objective
To establish a decision tree using preoperative PET/computed tomography (CT) parameters for detecting contralateral lymph node metastasis (CLNM) in oral cancer patients.

Methods
In total, 140 patients with a confirmed histopathological diagnosis of oral carcinoma showed fluorodeoxyglucose accumulation of contralateral lymph nodes in PET images. Of 260 lymph nodes, eight were metastatic. We compared metastatic and non-metastatic nodes using Fisher–Freeman-Halton exact and Fisher’s exact and Mann–Whitney U tests. The diagnostic performance was analyzed using receiver operating characteristic curves. We established a decision tree using exhaustive chi-squared automatic interaction detection algorithm.

Results
Five PET/CT parameters were significantly different between metastatic and non-metastatic nodes: the longest (P = 0.015) and shortest (P = 0.023) diameter, and the maximum standardized uptake values (SUVmax) of the contralateral node (P = 0.030), primary tumor (P < 0.001), and ipsilateral node (P < 0.001). The area under the curves of SUVmax of the primary tumor (0.887), ipsilateral node (0.886), and longest diameter (0.752) were the largest and these three parameters were used as predictive criteria in the decision tree. The accuracy of the decision tree was 97.7% with 100% sensitivity and 97.6% specificity.

Conclusion
Preoperative PET/CT imaging with a decision tree has the potential to diagnose CLNM in patients with oral cancer.
Rabbit systemic glucose metabolism map by total-body dynamic PET/CT technology
Authors: Wang Haochen , Xie Xue , Duan Yanhua , Chai Leiying , Li Kun , Qiu Jianfeng , Cheng Zhaoping 
Published: September 2023

Background
This study evaluated total-body glucose metabolism in a preclinical lab animal, the rabbit, by employing a dynamic glucose metabolic image obtained with total-body fluorine-18 fluorodeoxyglucose (18F-FDG) PET/computed tomography (PET/CT).

Methods
The dynamic total-body PET/CT system was used to obtain glucose metabolic imaging from 10 sedated body-matched rabbits. The standard uptake value (SUV) of 18F-FDG was used to evaluate glucose metabolism. In addition, the correlation between glucose metabolism and sexes was assessed, as well as metabolic differences between left- and right sides.

Results
We found significant distribution heterogeneity of glucose in several organs across the entire body. There were no significant metabolic differences between sexes and between bilateral sides in the 10 rabbits. Thereafter, we assayed the major organ SUV changes by dynamic PET/CT of the major organs. The heart, liver, and urinary system showed more 18F-FDG, whereas the skeletal muscle, brain, spinal cord, and lungs incorporated less 18F-FDG. The phenotype of 18F-FDG uptake was highly correlated with the physiological functions. The 18F-FDG accumulation in urinary system were observed which could reflect the renal parenchyma glucose metabolism indirectly. However, the low 18F-FDG uptake in the brain and spinal cord was due to sedation.

Conclusion
The total-body glucose metabolic atlas depicted with 18F-FDG dynamic PET/CT may be used as a reference for assessing pathological 18F-FDG uptake. Furthermore, this study could be a reference for preclinical research involving abnormality of glucose metabolism.
Training program intervention to encourage physical activity for health in people with transtibial amputation: A feasibility study
Authors: Asher Miranda , Strike Siobhan , Diss Ceri 
Published: September 2023

Background:
People with transtibial amputation (PTTA) would benefit from increased physical activity levels (PAL) but generic programs developed to support increased PAL do not address the barriers which PTTA experience.

Objective:
To evaluate the effect of a 12-week training program, developed for PTTA, on their PAL.

Methods:
Ten PTTA participated in a 12-week training program, which involved one instructor-led supervised group session per week. The program incorporated balance, flexibility, cardiovascular endurance, strength, and agility, as well as educational elements. Personalized starting level and progression intensity were based on the instructor's assessment in the first training session. The effect of the intervention on PAL (self-report questionnaire and accelerometer), fitness, walking symmetry, and adverse effects was determined by analysis of variance before and after the intervention.

Results:
There was a significant increase in self-reported time in moderate-intensity activity and accelerometer-measured step count and time in movement after the program compared with baseline (p = 0.02). The distance walked in the Six-Minute Walk Test (6MWT) (p < 0.001), time to perform agility test (p = 0.01), and lower-limb strength power (p = 0.01) and endurance (p = 0.01) were significantly greater after the program, and no adverse effects were identified.

Conclusions:
This study demonstrated an intervention designed specifically for PTTA that can increase PAL.
Factors associated with enrollment into differentiated service delivery model among adults with HIV in Kenya
Authors: Lavoie Marie-Claude C. , Koech Emily , Blanco Natalia , Wangusi Rebecca , Jumbe Marline , Kimonye Francis , Ndaga Angela , Ndichu Geofrey , Makokha Violet , Awuor Patrick , Momanyi Emmah , Oyuga Roseline , Nzyoka Sarah , Mutisya Immaculate , Joseph Rachel , Miruka Fredrick , Musingila Paul , Stafford Kristen A. , Lascko Taylor , Ngunu Carol , Owino Elizabeth , Kiplangat Anthony , Kepha Abuya , Ng’eno Caroline 
Published: September 2023

Introduction:
Differentiated service delivery (DSD) such as multimonth dispensing (MMD) aims to provide client-centered HIV services, while reducing the workload within health facilities. We assessed individual and facility factors associated with receiving more than three MMD and switching from ≥3MMD back to <3MMD in Kenya.

Methods:
We conducted a retrospective cohort study of clients eligible for DSD between July 2017 and December 2019. A random sample of clients eligible for DSD was selected from 32 randomly selected facilities located in Nairobi, Kisii, and Migori counties. We used a multilevel Poisson regression model to assess the factors associated with receiving ≥3MMD, and with switching from ≥3MMD back to <3MMD.

Results:
A total of 3501 clients eligible for ≥3MMD were included in our analysis: 1808 (51.6%) were receiving care in Nairobi County and the remaining 1693 (48.4%) in Kisii and Migori counties. Overall, 65% of clients were enrolled in ≥3MMD at the time of entry into the cohort. In the multivariable model, younger age (20–24; 25–29; 30–34 vs. 50 or more years) and switching ART regimen was significantly associated with a lower likelihood of ≥3MMD uptake. Factors associated with a higher likelihood of enrollment in ≥3MMD included receiving DTG vs. EFV-based ART regimen (aRR: 1.10; 95% confidence interval: 1.05–1.15).

Conclusion:
Client-level characteristics are associated with being on ≥3MMD and the likelihood of switching from ≥3MMD to <3MMD. Monitoring DSD enrollment across different populations is critical to successfully implementing these models continually.
Social Support Assets and Needs of Underrepresented Students Participating in Health Sciences Pathways Programs in Birmingham, Alabama
Authors: McCollum C. Greer , Carodine Alyssa , Chiedo Ashleigh , Penney Brooke , Long Dustin , Blumenfeld Rebecca , Smith Angela , Hill Samantha , Herbey Ivan Ivanovich , Rana Aadia , Elopre Latesha 
Published: September 2023

Background:
Using the Asset Bundle Model, we sought to understand the social support assets and needs of underrepresented minority (URM) high school, undergraduate, and graduate students.

Setting:
Study participants were or had participated in health sciences pathway programs at Birmingham City Schools and/or the University of Alabama at Birmingham.

Methods:
We took a concurrent mixed methods approach to conduct an environmental scan of health science pathway programs in the Birmingham, AL area. Four focus groups were conducted between November 2022 and January 2023, and a 225-item online survey was administered between November 4, 2022, and February 4, 2023. Both tools collected data from high school, undergraduate, and graduate students to examine key components of existing health care pathways programs for URMs and identify barriers and facilitators to successful implementation of such programs.

Results:
Twenty-two students participated in the focus groups, and 168 individuals responded to the survey. Both focus group participants and interview respondents were primarily URMs (eg, 68.2% and 65.7% identified as Black or African American, respectively). Survey responses and focus group discussions showed that, overall, undergraduate and graduate students programs develop more robust identities as future health care professionals through friendships and institutional supports, expand their networks more broadly through mentorship, and feel more supported by family members in their academic endeavors than high school students.

Conclusions:
Health science pathway programs for URMs should facilitate and bolster social supports for students, especially those in high school, to enhance persistence through education and into the workforce.
Building Indigenuity, Generating HIV Science: An HIV/AIDS Research Training Program for Undergraduate and Graduate Indigenous Scholars (BIG HART)
Authors: Balkus Jennifer E. , Conde Marcus , Lewin Anya , Walters Karina L. 
Published: September 2023

Introduction:
Although great heterogeneity and resilience exist among American Indians and Alaska Natives, Native Hawaiians and other Pacific Islanders, and Indigenous Latinx Populations across the United States, epidemiological data demonstrate these groups share a troubling commonality with respect to persistent health inequities, including HIV. A strong network of highly trained and productive Indigenous scientists dedicated to research that is culturally grounded is one component of a multifaceted approach that would contribute to ameliorating HIV-related disparities among Indigenous populations.

Methods:
Building on the only long-standing Indigenous-specific HIV/AIDS mentorship program in the United States—the Indigenous HIV/AIDS Research Training Program and with support from the CFAR Diversity, Equity, and Inclusion Pathway Initiative, the University of Washington/Fred Hutch CFAR developed and launched the Building Indigenuity, Generating HIV Science: HIV/AIDS Research Training Program (BIG HART) to introduce undergraduate and graduate Indigenous scholars to the field of HIV research.

Results:
The BIG HART program includes a seminar series to introduce undergraduate and graduate Indigenous scholars to the field of HIV research, opportunities to connect scholars with Indigenous mentors and provide networking opportunities to facilitate training opportunities related to HIV science, and complementary training for mentors to enhance their knowledge and training related to mentoring across difference, with a specific focus on mentoring Indigenous scholars.

Conclusions:
The BIG HART program is an important starting point toward building a sustainable program to attract Indigenous scholars in the field of HIV and grow and empower the next generation of Indigenous HIV scientists.
Glycosylation and Crowded Membrane Effects on Influenza Neuraminidase Stability and Dynamics
Authors: Seitz Christian , Deveci İlker , McCammon J. Andrew 
Published: September 2023

AbstractAll protein simulations are conducted with varying degrees of simplifications, oftentimes with unknown ramifications on how these simplifications affect the interpretability of the results. In this work we investigated how protein glycosylation and lateral crowding effects modulate an array of properties characterizing the stability and dynamics of influenza neuraminidase. We constructed three systems: 1) Glycosylated neuraminidase in a whole virion (i.e. crowded membrane) environment 2) Glycosylated neuraminidase in its own lipid bilayer 3) Unglycosylated neuraminidase in its own lipid bilayer. We saw that glycans tend to stabilize the protein structure and reduce its conformational flexibility while restricting solvent movement. Conversely, a crowded membrane environment encouraged exploration of the free energy landscape and a large scale conformational change while making the protein structure more compact. Understanding these effects informs what factors one must consider while attempting to recapture the desired level of physical accuracy.TOC figureTOC. Schematic of the three systems used here. (A) 2009-H1N1-ungly is the unglycosylated, single protein NA system. (B) 2009-H1N1-gly is the glycosylated, single protein NA system. (C) 2009-H1N1-vir is the NA in the virion context.
Reduced SV2A and GABAAreceptor levels in the brains of type 2 diabetic rats revealed by [18F]SDM-8 and [18F]flumazenil PET
Authors: Kong Yanyan , Xie Fang , Wang Xiuzhe , Zuo Chuantao , Shi Kuangyu , Rominger Axel , Huang Qi , Xiao Jianfei , Jiang Donglang , Guan Yihui , Ni Ruiqing 
Published: September 2023

AbstractPurposeType 2 diabetes mellitus (T2DM) is associated with a greater risk of Alzheimer’s disease. Synaptic impairment and protein aggregates have been reported in the brains of T2DM models. Here, we assessed whether neurodegenerative changes in synaptic vesicle 2A (SV2A), γ;-aminobutyric acid type A (GABAA) receptor, amyloid-β, tau and receptor for advanced glycosylation end product (RAGE) can be detected in vivo in T2DM rats.MethodsPositron emission tomography (PET) using [18F]SDM-8 (SV2A), [18F]flumazenil (GABAAreceptor), [18F]florbetapir (amyloid-β), [18F]PM-PBB3 (tau), and [18F]FPS-ZM1 (RAGE) was carried out in 12-month-old diabetic Zucker diabetic fatty (ZDF) and Sprague□Dawley (SD) rats. Proteomic profiling and pathway analysis of the hippocampus of ZDF and SD rats were performed.ResultsReduced cortical [18F]SDM-8 and cortical and hippocampal [18F]flumazenil uptake were observed in 12-month-old ZDF rats compared to SD rats. [18F]florbetapir and [18F]PM-PBB3 uptake were comparable in the brains of 12-month-old ZDF rats and SD rats.ConclusionThe findings provide in vivo evidence for regional reductions in SV2A and GABAAreceptor levels in the brains of aged T2DM ZDF rats.
Thetidyomicsecosystem: Enhancing omic data analyses
Authors: Hutchison William J. , Keyes Timothy J. ,   The tidyomics Consortium, Crowell Helena L. , Serizay Jacques , Soneson Charlotte , Davis Eric S. , Sato Noriaki , Moses Lambda , Tarlinton Boyd , Nahid Abdullah A. , Kosmac Miha , Clayssen Quentin , Yuan Victor , Mu Wancen , Park Ji-Eun , Mamede Izabela , Ryu Min Hyung , Axisa Pierre-Paul , Paiz Paulina , Poon Chi-Lam , Tang Ming , Gottardo Raphael , Morgan Martin , Lee Stuart , Lawrence Michael , Hicks Stephanie C. , Nolan Garry P. , Davis Kara L. , Papenfuss Anthony T. , Love Michael I. , Mangiola Stefano 
Published: September 2023

AbstractThe growth of omic data presents evolving challenges in data manipulation, analysis, and integration. Addressing these challenges, Bioconductor1provides an extensive community-driven biological data analysis platform. Meanwhile, tidy R programming2offers a revolutionary standard for data organisation and manipulation. Here, we present thetidyomicssoftware ecosystem, bridging Bioconductor to the tidy R paradigm. This ecosystem aims to streamline omic analysis, ease learning, and encourage cross-disciplinary collaborations. We demonstrate the effectiveness oftidyomicsby analysing 7.5 million peripheral blood mononuclear cells from the Human Cell Atlas3, spanning six data frameworks and ten analysis tools.
Effects of Neighboring Phosphorylation Events on the Affinities of pT181-Tau Antibodies
Authors: Min Sehong , Mohallem Rodrigo , Aryal Uma K , Kinzer-Ursem Tamara L. , Rochet Jean-Christophe 
Published: September 2023

ABSTRACTA tau variant phosphorylated on threonine 181 (pT181-tau) has been widely investigated as a potential Alzheimer’s disease (AD) biomarker in cerebrospinal fluid (CSF) and blood. pT181-tau is present in neurofibrillary tangles (NFTs) of AD brains, and CSF levels of pT181-tau correlate with overall NFT burden. Various immuno-based analytical methods, including Western blotting and ELISA, have been used to quantify pT181-tau in human biofluids. The reliability of these methods depends on the affinity and binding specificity of the antibodies used to measure pT181-tau levels. Although both of these properties could in principle be affected by phosphorylation within or near the antibody’s cognate antigen, such effects have not been extensively studied. Here, we developed a biolayer interferometry assay to determine the degree to which the affinity of pT181-tau antibodies is altered by the phosphorylation of serine or threonine residues near the target epitope. Our results revealed that phosphorylation near T181 negatively affected the binding of pT181-tau antibodies to their cognate antigen to varying degrees. In particular, two of three antibodies tested showed a complete loss of affinity for the pT181 target when S184 or S185 was phosphorylated. These findings highlight the importance of selecting antibodies that have been thoroughly characterized in terms of affinity and binding specificity, addressing the potential disruptive effects of post-translational modifications in the epitope region, to ensure accurate biomarker quantitation.
The Effect of Sunlight Intensity on Flower Opening Time and Exposure Duration in Rice (Oryza sativassp.indica) Landraces
Authors: Deb Debal , Dutta Sreejata , Nauri Mahendra 
Published: September 2023

AbstractRecords of sunlight intensity at anthesis of 388 rice landraces (with 32 replicated populations), flowering in the short-day season of 2022, reveal that under cloudy condition, the rice florets tend to open later, or the sunrise-to-anthesis duration (SAD) is longer when rice florets open than at sunny period. This difference in the length of SAD was statistically highly significant (p< 0.0001), confirmed by two sample permutation test with 10,000 iterations. This finding corroborates our general observation previously reported from a larger set of 1114 landraces (including the 388 landraces in this study). However, the intensity of sunlight at the flower opening time (FOT) may not remain uniformly sunny (high illuminance) or cloudy (low illuminance, < 40000 lux) until the flower closing time (FCT). To understand the effect of uniformly low sunlight intensity, we subsequently recorded solar illuminance at FOT of 33 landrace populations (including 8 repeats). Half of each population was kept under artificial shade, compared to the other half exposed to sunlight. This experiment revealed that low illuminance, mimicking overcast days, significantly (p< 0.01) delays FOT and lengthens SAD, corroborating the pattern detected in our earlier findings. Permutation tests with 10,000 iterations decisively confirms (p< 0.0001) the prolongation of SAD under shade and cloudy condition. Experimental shading has an indeterminate effect on FED of the same landraces. We surmise that the delayed FOT during natural cloudy period is an adaptation in rice plants in anticipation of rain, for protection of the pollen from rainwash.
The optimization ofSalmonellasurveillance programmes for pullet and layer farms using local farm density as a risk factor
Authors: Hobbelen Peter H.F. , Hagenaars Thomas J. , Markovich Michal Peri , Bellaiche Michel , Giovannini Armando , Massis Fabrizio De , de Koeijer Aline 
Published: September 2023

AbstractHuman salmonellosis cases are often caused by Salmonella serovars Enteritidis and Typhimurium and a large percentage of Salmonella outbreaks is associated with the consumption of eggs and egg products. For this reason, many countries implemented general surveillance programmes for the detection and control ofSalmonellaon pullet and layer farms. The infection risk however varies between farms and the identification of risk factors forSalmonellainfection may be used to improve the performance of these surveillance programmes. The aims of this study are therefore to determine 1) whether local farm density is a risk factor for the infection of pullet and layer farms bySalmonellaEnteritidis and Typhimurium and 2) whether the sampling effort of surveillance programmes can be reduced by accounting for this risk factor, while still providing sufficient control of target serovars Enteritidis and Typhimurium. To assess the importance of local farm density as a risk factor, we fitted different transmission kernels to Israeli surveillance data during the period from June 2017 to April 2019. The analysis showed that the distance to infected farms significantly increases the infection risk by serovar Enteritidis within an approximately 4 km radius and by Typhimurium within an approximately 0.3 km radius. We subsequently used these kernels to derive a model for the between-farm R0and used it to optimise a surveillance programme that subdivided layer farms into groups at low and at high risk of between-farm transmission based on the local farm density and allowed the sampling frequency to vary between these groups. In this design, the pullet farms were always sampled one week prior to pullet distribution. Our analysis showed that the risk-based surveillance programme was able to keep the between-farm R0of serovars Enteritidis and Typhimurium below 1 for all pullet and layer farms, using a sampling effort that was reduced by 32% compared to the currently implemented surveillance programme in Israel. The results of our study therefore indicate that local farm density is an important risk factor for infection of pullet and layer farms bySalmonellaEnteritridis and Typhimurium and can be used to improve the performance of surveillance programmes.