bluuebunny/crossref_metadata_2025_split huggingface dataset:
Validating a multi-locus metabarcoding approach for characterizing mixed-pollen samples
Authors: Wizenberg Sydney B. , Newburn Laura R. , Pepinelli Mateus , Conflitti Ida M. , Richardson Rodney T. , Hoover Shelley E. R. , Currie Robert W. , Giovenazzo Pierre , Zayed Amro 
Published: November 2023

Abstract
Background
The mutualistic interaction between entomophilous plants and pollinators is fundamental to the structure of most terrestrial ecosystems. The sensitive nature of this relationship has been disrupted by anthropogenic modifications to natural landscapes, warranting development of new methods for exploring this trophic interaction. Characterizing the composition of pollen collected by pollinators, e.g. Apis mellifera, is a common means of exploring this relationship, but traditional methods of microscopic pollen assessment are laborious and limited in their scope. The development of pollen metabarcoding as a method of rapidly characterizing the abundance and diversity of pollen within mixed samples presents a new frontier for this type of work, but metabarcoding may have limitations, and validation is warranted before any suite of primers can be confidently used in a research program. We set out to evaluate the utility of an integrative approach, using a set of established primers (ITS2 and rbcL) versus melissopalynological analysis for characterizing 27 mixed-pollen samples from agricultural sites across Canada.

Results
Both individual markers performed well relative to melissopalynology at the family level with decreases in the strength of correlation and linear model fits at the genus level. Integrating data from both markers together via a multi-locus approach provided the best rank-based correlation between metagenetic and melissopalynological data at both the genus (ρ = 0.659; p < 0.001) and family level (ρ = 0.830; p < 0.001). Species accumulation curves indicated that, after controlling for sampling effort, melissopalynological characterization provides similar or higher species richness estimates than either marker. The higher number of plant species discovered via the metabarcoding approach simply reflects the vastly greater sampling effort in comparison to melissopalynology.

Conclusions
Pollen metabarcoding performed well at characterizing the composition of mixed pollen samples relative to a traditional melissopalynological approach. Limitations to the quantitative application of this method can be addressed by adopting a multi-locus approach that integrates information from multiple markers.
Surgical healing beyond the scalpel: exploring the impact of depressive symptoms on functional recovery in total knee arthroplasty patients
Authors: Neelaraju Harshith , Gangaiah Mahesh , Mittal Prabhat 
Published: November 2023

Abstract
Background
Numerous recent studies have explored the association between the mental health condition of patients before surgery and the outcomes of total knee arthroplasty. The objective of this study was to determine the prevalence of depressive symptoms among individuals undergoing total knee arthroplasty and to investigate the impact of pre-operative depressive symptoms as a significant and independent predictor on various health-related quality of life measures for patients undergoing knee surgery.

Material and methods
During the period spanning from August 2019 to May 2020, an orthopedic database was established for the purpose of assessing patients' conditions before their surgeries. The data collection process occurred at three distinct intervals: prior to the surgery, as well as at the third and sixth months following the surgical procedure. In this study, we undertook an evaluation of both pre-operative and postoperative depressive symptoms, as well as functional status, utilizing various self-report measures. These measures included the Becks Depression Scale, the Western Ontario and McMaster Universities Osteoarthritis Index, and the Knee Society Clinical Rating System.

Results
A total of 150 patients were included in the study. The proportion of patients who were severely distressed decreased from 99% (149) at the baseline assessment to 76% (114) who had mild depression and 24% (36) at borderline at 3-months of follow-up. At 6-month follow-up period, 85% (128) patients were classified as normal, with 15% (22) displaying mild distress levels.

Conclusions
Patients experiencing depression exhibited notable enhancements in various outcome measures. The findings from this study underscore a two-way relationship between mental health and surgical outcomes. Specifically, the surgical intervention yielded significant improvements in mental health status. Conversely, poorer pre-operative mental health status emerged as a predictive factor for comparatively less favorable outcomes stemming from the surgery.
CD276-CAR T cells and Dual-CAR T cells targeting CD276/FGFR4 promote rhabdomyosarcoma clearance in orthotopic mouse models
Authors: Timpanaro Andrea , Piccand Caroline , Dzhumashev Dzhangar , Anton-Joseph Stenija , Robbi Andrea , Moser Janine , Rössler Jochen , Bernasconi Michele 
Published: November 2023

Abstract
Background
Rhabdomyosarcoma (RMS) is the most common soft tissue sarcoma in childhood, whose prognosis is still poor especially for metastatic, high-grade, and relapsed RMS. New treatments are urgently needed, especially systemic therapies. Chimeric Antigen Receptor T cells (CAR Ts) are very effective against hematological malignancies, but their efficacy against solid tumors needs to be improved. CD276 (B7-H3) is a target upregulated in RMS and detected at low levels in normal tissues. FGFR4 is a very specific target for RMS. Here, we optimized CAR Ts for these two targets, alone or in combination, and tested their anti-tumor activity in vitro and in vivo.

Methods
Four different single-domain antibodies were used to select the most specific FGFR4-CAR construct. RMS cell killing and cytokine production by CD276- and FGFR4-CAR Ts expressing CD8α or CD28 HD/TM domains in combination with 4-1BB and/or CD28 co-stimulatory domains were tested in vitro. The most effective CD276- and FGFR4-CAR Ts were used to generate Dual-CAR Ts. Tumor killing was evaluated in vivo in three orthotopic RMS mouse models.

Results
CD276.V-CAR Ts (276.MG.CD28HD/TM.CD28CSD.3ζ) showed the strongest killing of RMS cells, and the highest release of IFN-γ and Granzyme B in vitro. FGFR4.V-CAR Ts (F8-FR4.CD28HD/TM.CD28CSD.3ζ) showed the most specific killing. CD276-CAR Ts successfully eradicated RD- and Rh4-derived RMS tumors in vivo, achieving complete remission in 3/5 and 5/5 mice, respectively. In CD276low JR-tumors, however, they achieved complete remission in only 1/5 mice. FGFR4 CAR Ts instead delayed Rh4 tumor growth. Dual-CAR Ts promoted Rh4-tumors clearance in 5/5 mice.

Conclusions
CD276- and CD276/FGFR4-directed CAR Ts showed effective RMS cell killing in vitro and eradication of CD276high RMS tumors in vivo. CD276low tumors escaped the therapy highlighting a correlation between antigen density and effectiveness. FGFR4-CAR Ts showed specific killing in vitro but could only delay RMS growth in vivo. Our results demonstrate that combined expression of CD276-CAR with other CAR does not reduce its benefit. Introducing immunotherapy with CD276-CAR Ts in RMS seems to be feasible and promising, although CAR constructs design and target combinations have to be further improved to eradicate tumors with low target expression.
Activities critical to success and growth of clinical trials networks. What is needed and how are we doing? An Australian and New Zealand perspective
Authors: Sanders Megan , Goulding Karen , Oakley Ed , Reidlinger Donna , Groom Katie M 
Published: November 2023

Abstract
Background
Clinical trial evidence underpins evidence-based medicine and the improvement of healthcare worldwide. In Australasia, a significant proportion of clinical trials are conducted by geographically dispersed and multidisciplinary clinical researchers under the auspices of Clinical Trials Networks (CTNs). These groups play an important role in contributing to evidence-based medicine, primarily by conducting investigator-initiated clinical trials. Despite their clear benefits in terms of return on investment, CTNs suffer significant challenges.

Methods
We conducted surveys and focus groups with Australian and New Zealand CTNs to identifying the activities and attributes that enable CTNs to operate successfully. Based on our findings, we then conducted further surveys of Australian and New Zealand CTNs to identify the prevalence of these success factors in existing CTNs.

Results
Our focus groups identified three key themes associated with success and growth of a CTN: engaged membership, established infrastructure, and sustainability; and thirteen critical success factors: shared vision and motivation; strong leaders, governance and succession planning; an executive officer; sustainable funding for operations; effective communication; diverse representation and consumer input; transparent processes; a strong pipeline of trials; a reputable and recognised CTN brand; innovation and adaption; an effective group of network sites with a skilled workforce; embedded trials and prioritisation of research. These key themes and the relevant key areas were presented to 30 CTNs. Two factors were almost universally present in CTNs, reflecting the importance of these attributes: the presence of an executive officer, and a strong pipeline of trials. Three factors had a particularly low prevalence: sustainable funding for operations, effective communication, and embedded trials.

Conclusions
By supporting both emerging and established CTNs to achieve critical success factors, we can improve the efficiency of CTNs to continue to contribute and expand their clinical trial activities. Particular focus needs to be on finding sustainable funding for CTNs, and raising awareness of the critical role undertaken by CTNs to improve healthcare and health outcomes.
Peer PrEP referral + HIV self-test delivery for PrEP initiation among young Kenyan women: study protocol for a hybrid cluster-randomized controlled trial
Authors: Wairimu Njeri , Malen Rachel C. , Reedy Adriana M. , Mogere Peter , Njeru Irene , Culquichicón Carlos , McGowan Maureen , Gao Fei , Baeten Jared M. , Ngure Kenneth , Ortblad Katrina F. 
Published: November 2023

Abstract
Background
Oral HIV pre-exposure prophylaxis (PrEP) for HIV prevention is highly effective, but uptake remains low in Africa, especially among young women who are a priority population for HIV prevention services. HIV self-testing (HIVST) has been proven to increase HIV testing in diverse populations but has been underutilized to support linkage to HIV prevention services. Most young women who initiate PrEP in Africa do so through informal peer referral. We wanted to test a model of formalized peer referral enhanced with HIVST delivery among young Kenyan women.

Methods
The Peer PrEP Trial is a two-arm hybrid effectiveness-implementation cluster-randomized controlled trial being conducted in central Kenya. Eligible participants (i.e., peer providers, n = 80) are women (≥ 16–24 years) refilling or initiating PrEP at public healthcare clinics who can identify at least four peers who could benefit from PrEP and not enrolled in another HIV study. Peer providers will be 1:1 randomized to (1) formal peer PrEP referral + HIVST delivery, where they will be encouraged to refer four peers (i.e., peer clients, ≥ 16–24 years) using educational materials and HIVST kits (two per peer client), or (2) informal peer PrEP referral, where they are encouraged to refer four peer clients using informal word-of-mouth referral. In both arms, peer providers will deliver a standard PrEP referral card with information on nearby public clinics delivering PrEP services. Peer providers will complete surveys at baseline and 3 months; peer clients will complete surveys at 3 months. Our primary outcome is PrEP initiation among peer clients, as reported by peer providers at 3 months. Secondary outcomes include PrEP continuation (any refilling), HIV testing (past 3 months), sexual behaviors (past month), and PrEP adherence (past month) among peer clients, as reported by both peer providers and clients at 3 months. Implementation outcomes will include participants’ perceived acceptability, appropriateness, and feasibility of the intervention as well assessments of the intervention’s fidelity and cost.

Discussion
Evidence from this trial will help us understand how HIVST could support health systems by facilitating linkage to PrEP services among young women who could benefit in Kenya and similar settings.

Trial registration
ClinicalTrials.gov NCT04982250. Registered on July 29, 2021.
Assessment of the performance of haematological and non-invasive fibrotic indices for the monitoring of chronic HBV infection: a pilot study in a Ghanaian population
Authors: Nyarko Eric N. Y. , Obirikorang Christian , Owiredu W. K. B. A. , Adu Evans Asamoah , Acheampong Emmanuel 
Published: November 2023

Abstract
Objective
Haematological and liver fibrotic markers could be appreciably utilized for effective monitoring of Chronic Hepatitis B viral (HBV) infection, thereby increasing patient’s treatment outcome. The objective of this study was to assess the applicability of complete blood count (CBC) and non-invasive liver-fibrotic indices as markers of prognostic outcome and monitoring in HBV infections.

Results
Significant differences in levels of white cell and differentials counts, red blood cell count, hemoglobin indices, and platelet indices were observed between HBV-infected patients (cases) and uninfected persons (controls). Levels of haemoglobin (Hb), total white blood cells (tWBC), neutrophils, monocytes, platelets, and Platelet Distribution width (PDW) were significantly lower (p < 0.05) in the cases compared to the controls. Total and indirect bilirubin; De-Ritis ratio, Aspartate transaminase to platelet ratio index (APRI) and RDW-to-platelet ratio (RPR) were elevated in cases compared with controls (p-value < 0.05). In a multivariate adjusted model to test the significance of markers, Hemoglobin Index (beta coefficient = − 0.876, p-value < 0.001), NLR (beta coefficient = − 0.839, p-value < 0.001), MPV_10000 (beta coefficient = − 0.333, p-value < 0.001) and Albumin (beta coefficient = − 0.059, p-value = 0.014), were associated with HBV infection status. Receiver operative characteristics curve analysis showed Hemoglobin Index (AUC = 0.744) and MPV_10000 (AUC = 0.730) as better prognostic markers for HBV-infection.
Identification of novel diagnostic panel for mild cognitive impairment and Alzheimer’s disease: findings based on urine proteomics and machine learning
Authors: Wang Yuye , Sun Yu , Wang Yu , Jia Shuhong , Qiao Yanan , Zhou Zhi , Shao Wen , Zhang Xiangfei , Guo Jing , Zhang Bin , Niu Xiaoqian , Wang Yi , Peng Dantao 
Published: November 2023

Abstract
Background
Alzheimer’s disease is a prevalent disease with a heavy global burden. Proteomics is the systematic study of proteins and peptides to provide comprehensive descriptions. Aiming to obtain a more accurate and convenient clinical diagnosis, researchers are working for better biomarkers. Urine is more convenient which could reflect the change of disease at an earlier stage. Thus, we conducted a cross-sectional study to investigate novel diagnostic panels.

Methods
We firstly enrolled participants from China-Japan Friendship Hospital from April 2022 to November 2022, collected urine samples, and conducted an LC–MS/MS analysis. In parallel, clinical data were collected, and clinical examinations were performed. After statistical and bioinformatics analyses, significant risk factors and differential urinary proteins were determined. We attempt to investigate diagnostic panels based on machine learning including LASSO and SVM.

Results
Fifty-seven AD patients, 43 MCI patients, and 62 CN subjects were enrolled. A total of 3366 proteins were identified, and 608 urine proteins were finally included in the analysis. There were 33 significantly differential proteins between the AD and CN groups and 15 significantly differential proteins between the MCI and CN groups. AD diagnostic panel included DDC, CTSC, EHD4, GSTA3, SLC44A4, GNS, GSTA1, ANXA4, PLD3, CTSH, HP, RPS3, CPVL, age, and APOE ε4 with an AUC of 0.9989 in the training test and 0.8824 in the test set while MCI diagnostic panel included TUBB, SUCLG2, PROCR, TCP1, ACE, FLOT2, EHD4, PROZ, C9, SERPINA3, age, and APOE ε4 with an AUC of 0.9985 in the training test and 0.8143 in the test set. Besides, diagnostic proteins were weakly correlated with cognitive functions.

Conclusions
In conclusion, the procedure is convenient, non-invasive, and useful for diagnosis, which could assist physicians in differentiating AD and MCI from CN.
Correlation analysis of clinical, pathological, imaging and genetic features of ground-glass nodule featured lung adenocarcinomas between high-risk and non-high-risk individuals
Authors: Ren Jing , Wang Yuan , Liu Chunrong , Yang Lan , Men Xinlu , Qiu Zhixin 
Published: November 2023

Abstract
Background
Early stage lung adenocarcinomas manifested as ground-glass nodules (GGNs) are increasingly being detected, but screening and diagnosis for GGN-featured lung adenocarcinomas in different risk populations reach no agreement.

Objectives
To analyze the clinical, pathological, imaging and genetic features of GGN-featured lung adenocarcinomas on high-resolution computed tomography (HRCT) in different risk groups.

Methods
Include patients with GGNs on HRCT surgically diagnosed as lung adenocarcinoma in the West China Hospital, Sichuan University from 2009 to 2021, and their clinical, pathological, imaging and gene sequencing data.

Results
According to Chinese Expert Consensus on Screening and Management of Lung Cancer, 1,800 patients with GGN-featured lung adenocarcinoma, 545 males (incl. 269 smokers) and 1,255 females (incl. 16 smokers), were divided into high-risk (509) and non-high-risk (1,291) groups. Among them, 1,095 were detected via physical examination. The mean age at diagnosis was 54.78 (23–84) and the mean time from detection to diagnosis was 9.59 months. There were more males than females in the high-risk group [288 (56.58%) vs 221 (43.42%)], just the opposite in the non-high-risk group [1,034 (80.09%) vs 257 (19.91%)] (both P < 0.001). No statistical difference was found in GGN detection way (P > 0.05). The frequency of invasive adenocarcinoma was higher in the high-risk group, while those of precursor lesions and minimally invasive adenocarcinoma were higher in the non-high-risk group (all P < 0.001). The preoperative follow-up time in the non-high-risk group was shorter (P < 0.05). A total of 711 gene mutations were observed in 473 patients with a ratio of non-high-risk to high-risk of 494:217. The incidence of EGFR mutation was not statistically significant (P = 0.824), while those of TP53 and KRAS mutations were higher in the high-risk group (P < 0.05).

Conclusions
GGN-featured lung adenocarcinoma is dominated by non-high-risk female patients. Shorter preoperative follow-up in the non-high-risk group and no statistical difference in GGN detection way suggests the existing screening criteria for high-risk population may not suit GGN-featured lung cancer. In addition, the incidences of KRAS and TP53 mutations are higher in the high-risk group.
Nutrition transition, double burden of malnutrition, and urbanization patterns in secondary cities of Bangladesh, Kenya and Rwanda
Authors: Barth-Jaeggi Tanja , Speich Cornelia , Havugimana Cassien , Bayisenge Francine , Kimenju Simon , Omondi Wilfred , Pasha S. Fuad , Islam Shahidul , van Zutphen-Küffer Kesso Gabrielle , van den Berg Sophie , Barjolle Dominique , Pannatier Marnie , Prytherch Helen 
Published: November 2023

Abstract
Background
By 2050, approximately 68% of the global population will live in cities, but nutrition data on urban populations of low- and middle-income countries are scarce. Fast growing secondary cities, combining characteristics and hurdles of urban and rural settings, are hotspots for the double burden of malnutrition. The Nutrition in City Ecosystems (NICE) project focuses on 6 secondary cities in Bangladesh, Kenya and Rwanda, to improve health and nutrition, and reduce poverty. To assess the baseline situation and guide future interventions, food insecurity, dietary diversity, nutrition status, and food production and purchasing patterns were explored.

Methods
In a cross-sectional study design, data were collected from urban and peri-urban households of Dinajpur and Rangpur in Bangladesh, Bungoma and Busia in Kenya, and Rubavu and Rusizi in Rwanda. Approximately 1200 households, in neighborhoods prone to malnutrition, were involved from April to June 2021. We assessed Household Food Insecurity Access Score (HFIAS), both current and before COVID-19, Household Dietary Diversity Score (HDDS), Minimum Dietary Diversity for Women (MDD-W), anthropometric measurements, household and socioeconomic information, and questions related to food production and consumer behavior. Further we collected secondary data on low birthweight and anemia during pregnancy.

Results
All cities experienced a substantial increase in food insecurity during the COVID-19 pandemic. Stunting rates in children under 5 years varied among the cities and ranged from 7.8% in Busia to 46.6% in Rubavu, while half of adult women were overweight (between 42.1% in Rusizi and 55.8% in Bungoma). Furthermore, many women did not consume an adequately diverse diet (MDD-W < 5 for 29.3% in Bangladesh, 47.5% in Kenya, and 67.0% in Rwanda), however many of the urban and peri-urban households were engaged in farming (58–78%).

Conclusions
The double burden of malnutrition is high in secondary cities and the COVID-19 pandemic has exacerbated levels of food insecurity. Demand for, and access to, an affordable healthy diverse diet that comprises local, nutritious, and agroecologically produced foods present a pathway for overcoming the complex challenges of malnutrition.
Utilization and short-term outcomes of percutaneous left atrial appendage occlusion in patients with cancer
Authors: Zhang Yaqi , Yang Zhuoran , Almani Muhammad U. , Soon-Shiong Raquel , Liu Bolun 
Published: November 2023

Abstract
Background
Percutaneous left atrial appendage occlusion (LAAO) has been rapidly evolving since FDA’s approval in 2015 and has become more of a same-day-discharge procedure. Cancer patient with atrial fibrillation/flutter (AF) population can benefit from the procedure but the in-hospital outcomes and readmission data were rarely studied.

Objectives
We investigated the utilization, in-hospital and readmission outcomes in cancer patients with AF who underwent LAAO.

Methods
Data were derived from the National Inpatient Sample and National Readmissions Database from 2016 to 2019. Patients with primary diagnosis of AF admitted for LAAO (ICD-10 code 02L73DK) were grouped by cancer as a secondary diagnosis. We assessed in-hospital mortality, length of stay, total hospital charges, and complications. Thirty-day readmission rates were compared.

Results
LAAO was performed in 60,380 patients with AF and 3% were cancer patients. There were no differences in in-hospital mortality and total hospital charges; however, cancer patients tended to have longer hospital stay (1.59 ± 0.11 vs. 1.32 ± 0.02, p = 0.013). Among complications, cancer patients had higher rates in open or percutaneous pericardial drainage (adjusted odds ratio [aOR] 2.38; 95% confidence interval [CI] 1.19–4.76) and major bleeding events (aOR 7.07; 95% CI 1.82–27.38). There was no statistical significance of 30-day readmission rates between patients with and without cancer (10.0% vs. 9.1%, p = 0.34). The most common readmission reason in cancer patients was gastrointestinal bleeding.

Conclusions
LAAO is a promising procedure in cancer patients complicated by AF with contraindication to anticoagulation. Readmission rate is comparable between patients with and without cancer.