bluuebunny/crossref_metadata_2025_split huggingface dataset:
Abstract B060: Clonal composition of αβ and γδ T cells in primary human neuroblastoma tumors – Is every child unique?
Authors: Verhoeven Bronte Manouk , Ye Kewei , Stenman Jakob , Kogner Per , Johnsen John Inge , Reina Oscar Bedoya , Kreslavskiy Taras , Baryawno Ninib 
Published: September 2024

Abstract
Alpha beta (ab) T cells are immune cells that play a key role in the adaptive immune system. Over the years many different ab T cell subtypes have been defined including cells with anti-tumor cytotoxic functions. Gamma delta (gd) T cells are considered the bridge between innate and adaptive immunity. While rules of antigen recognition by gd T cells remain poorly understood, this recognition takes place in the absence of classical antigen presentation on MHC molecules. In neuroblastoma (NB), the most common and deadly extracranial tumor in children, different subtypes of T cells have been identified in the tumor microenvironment (TME) and their presence is correlated to improved prognosis. However, it remains unknown whether T cells in the TME have clonally expanded, and if yes, which antigens they recognize. Our aim is thus to uncover the clonal composition of T cells in primary human NB tumors including to elucidate ligand recognition in gd T cells. To address these questions, we performed flow cytometry analysis to elucidate gd T cell composition in 14 patient samples, and additionally performed single-cell (sc) RNA/VDJ-seq experiments to characterize clonal composition and functional states of ab and gd T cells infiltrating NB tumors from 11 patients for which 4 had a matched blood sample. In patients' blood, as expected, most gd T cells detected were Vg9Vd2+ cells. In contrast, the majority of detected infiltrating gd T cells in NB tumors were Vd1+ cells. scRNA/VDJ-seq experiments revealed prominent clonal expansion of both ab and gd T cells varying between patients. Clonal expansion was particularly prominent for gd T cells in one female intermediate risk patient’s tumor where nearly half of the cells represented one of the two top expanded clones with unique Vd1 and Vd3 TCRs. Interestingly, we detected Vd1/ Vd3 expanded clones with both a clear cytotoxic signature and with a possible wound healing phenotype. Taken together, drastic clonal expansion of both ab and gd T cells in NB suggests that these cells may recognize antigens present in the TME providing possibilities for immunotherapy.
Citation Format: Bronte Manouk Verhoeven, Kewei Ye, Jakob Stenman, Per Kogner, John Inge Johnsen, Oscar Bedoya Reina, Taras Kreslavskiy, Ninib Baryawno. Clonal composition of αβ and γδ T cells in primary human neuroblastoma tumors – Is every child unique [abstract]. In: Proceedings of the AACR Special Conference in Cancer Research: Advances in Pediatric Cancer Research; 2024 Sep 5-8; Toronto, Ontario, Canada. Philadelphia (PA): AACR; Cancer Res 2024;84(17 Suppl):Abstract nr B060.
From Qumran Caves to Swiss Vaults
Authors: Justnes Årstein 
Published: September 2024

Abstract
When first announced, many of the post-2002 Dead Sea Scrolls-like fragments were depicted as experienced travelers having moved over long distances. Some of Martin Schøyen’s fragments had allegedly been to Bethlehem, Lebanon, and Zurich before they eventually came to Norway. According to Weston W. Fields, the so-called Butterfly fragment—William Kando’s fabled Genesis scroll—was first sent to Germany before it “made its way to the vault [in Switzerland]” in 1965 or 1966. Other fragments had traveled from Bethlehem to Beirut, from Beirut to Cyprus, and from Cyprus to Zurich, but no one seemed to know exactly how. In most cases the fragments “appeared,” “found/made their way,” “turned up,” “saw the light,” or “surfaced” in the fulness of time. More recently, the Israel Antiquities Authority’s (IAA) sensational (and unprovenanced) “Ishmael Papyrus” was even said to have “come to the awareness of epigraphists” 50 years after an unnamed Montana woman hung it on the wall in her living room. The fragment’s last trip from Montana to the IAA’s Dead Sea Scrolls lab managed to transform the living room decoration into a Dead Sea Scroll fragment of great scientific interest. In this article, I analyze some of these itineraries—the routes between the ideal starting point (Khirbet Qumran or, more specifically, Qumran Cave 4) and the ideal laundering point (Zurich, a Swiss vault, the IAA’s Dead Sea Scrolls lab)—and discuss their function. My main interest is to show how stories of long-distance mobility transform the status of fake and unprovenanced fragments.
“And He Gives Her a Bill of Divorcement”
Authors: Michaels Marc 
Published: September 2024

Abstract
This essay explores the halakhic precedents that can be drawn upon concerning the need for, and possible form of, a גט geṭ (Jewish religious divorce) when one of the parties involved has undergone gender transition. Does a geṭ need to be written at all? If so, can the transgender partner (in the case considered, the former husband) give a geṭ? If so, what names should be used on the geṭ? Here we examine the reactions of the various Jewish denominational movements to this growing societal phenomenon and study how the denominational setting impacts the answers to those questions.
Absent Women Philosophers from Past to Present in Indian Thought: Ṛṣikās, Sarojini Naidu, and Jaishree Odin
Authors: Ali Muzaffar , Shukla Richa , Rathour Mansi 
Published: September 2024

Abstract
This essay seeks to retrace, retrieve, recover, and reclaim the voices of women thinkers and philosophers throughout the history of Indian philosophy. The aim is to initiate a discussion on the conventional and ‘malestream’ character of established knowledge in philosophy. We focus on a few women thinkers to underline the fact that by acknowledging and elevating their previously erased and marginalized works, an alternative, and enriched, trajectory of the entire philosophical corpus of Indian thought is possible. To create a slice of such an alternate trajectory, we discuss the contributions of Ṛṣikās (women sages), Sarojini Naidu, and Jaishree Odin in the ancient, modern, and contemporary domains of Indian philosophy to argue and underline that these otherwise erased and absent women are thinking-beings actively involved in the give and take of philosophical progress in the Indian context.
Inference of single-cell network using mutual information for scRNA-seq data analysis
Authors: Chang Lan-Yun , Hao Ting-Yi , Wang Wei-Jie , Lin Chun-Yu 
Published: September 2024

Abstract
Background
With the advance in single-cell RNA sequencing (scRNA-seq) technology, deriving inherent biological system information from expression profiles at a single-cell resolution has become possible. It has been known that network modeling by estimating the associations between genes could better reveal dynamic changes in biological systems. However, accurately constructing a single-cell network (SCN) to capture the network architecture of each cell and further explore cell-to-cell heterogeneity remains challenging.

Results
We introduce SINUM, a method for constructing the SIngle-cell Network Using Mutual information, which estimates mutual information between any two genes from scRNA-seq data to determine whether they are dependent or independent in a specific cell. Experiments on various scRNA-seq datasets with different cell numbers based on eight performance indexes (e.g., adjusted rand index and F-measure index) validated the accuracy and robustness of SINUM in cell type identification, superior to the state-of-the-art SCN inference method. Additionally, the SINUM SCNs exhibit high overlap with the human interactome and possess the scale-free property.

Conclusions
SINUM presents a view of biological systems at the network level to detect cell-type marker genes/gene pairs and investigate time-dependent changes in gene associations during embryo development. Codes for SINUM are freely available at https://github.com/SysMednet/SINUM.
Perioperative pain management interventions in opioid user patients: an overview of reviews
Authors: Vadeghani Ava Tavakoli , Grant Margaret , Forget Patrice 
Published: September 2024

Abstract
Background
Every year, many opioid users undergo surgery, experiencing increased postoperative complications, inadequate pain control, and opioid-related adverse effects. This overview aims to summarise and critically assess the systematic reviews about perioperative pain management interventions, identify the knowledge gaps, and potentially provide high-quality recommendations to improve postoperative analgesia and surgical outcomes.

Methods
A systematic search was conducted from the following databases, PubMed, Cochrane Database of Systematic Reviews, Embase, APA PsycINFO, CINAHL, AMED, Scopus, PROSPERO, ProQuest, and Epistemonikos, in June 2023. Additionally, reference lists were reviewed. The identified studies were assessed based on eligibility criteria and data extracted by a self-designed form and two independent reviewers. Qualitative data were synthesised, and all included studies were assessed by The Assessment of Multiple Systematic Reviews 2 (AMSTAR 2) checklist.

Results
Nine studies were included. The methodological quality of the studies was mostly critically low. Various interventions were identified, including perioperative management of buprenorphine, ketamine administration, multimodal analgesia, higher doses of medications, patient education, and interprofessional collaboration. The level of certainty of the evidence ranged from very low to high. One high-quality study showed that ketamine administration may improve perioperative analgesia supported with moderate to very low-quality evidence, and low and critically low studies indicated the efficacy of perioperative continuation of buprenorphine with low to very low-quality evidence.

Conclusion
Perioperative continuation of buprenorphine and ketamine administration as a multimodal analgesia approach, with moderate to very low-quality evidence, improves pain management in opioid users and decreases opioid-related adverse effects. However, high-quality systematic reviews are required to fill the identified gaps in knowledge.
High expression of small nucleolar host gene RNA may predict poor prognosis of Hepatocellular carcinoma, based on systematic reviews and meta-analyses
Authors: Du Sheng-qi , Liu Ya-Tong , Yang Fen , Wang Pei-xue , Zhang Jun 
Published: September 2024

Abstract
Background
The prognosis of patients with hepatocellular cancer is substantially correlated with the abnormal expression of growing long non-coding RNA small nucleolar host gene RNA (SNHG) families in liver cancer tissues. This study aimed to examine the relationship between SNHG expression and liver cancer prognosis.

Methods
After searching six internet databases, pertinent manuscripts were found based on inclusion and exclusion criteria. To determine whether SNHG expression levels affect liver cancer prognosis, raw data were collected and hazard ratios (HRs) and odds ratios (ORs) were calculated. The results were examined for potential publication bias using the sensitivity analysis and Beeg’s test.

Results
Most SNHG family members were up-regulated in liver cancer tissues. High SNHG expression predicts poor liver cancer outcomes of, including overall survival (OS) (HR: 1.697, 95% confidence interval [CI]: 1.373–2.021), especially SNHG5 (the HR of OS is 4.74, 95%CI range from 1.35 to 6.64), progression-free survival (HR: 1.85, 95% CI: 1.25–2.73), tumor, node, metastasis (TNM) stage (OR: 1.696, 95% CI: 1.436–2.005), lymph node metastasis (OR: 2.383, 95% CI: 1.098–5.173), and tumor size (OR: 1363, 95% CI: 1.165–1.595). The OS results were found to be reliable and robust, as indicated by the sensitivity analysis. Additionally, Beeg’s test demonstrated the absence of any potential publication bias for each result.

Conclusion
In liver cancer tissues, most SNHGs are highly expressed, which may signal poor prognosis. SNHG has the potential to be an intriguing predictive marker and a prospective therapeutic target for liver cancer.
Food and beverage manufacturing and retailing company policies and commitments to improve the healthfulness of Canadian food environments
Authors: Gaucher-Holm Alexa , Chan Jasmine , Sacks Gary , Vaillancourt Caroline , Vergeer Laura , Potvin Kent Monique , Olstad Dana Lee , Vanderlee Lana 
Published: September 2024

Abstract
Background
Food and beverage companies play a central role in shaping the healthfulness of food environments.

Methods
The BIA-Obesity tool was used to evaluate and benchmark the specificity, comprehensiveness and transparency of the food environment-related policies and commitments of leading food and beverage manufacturing and retailing companies in Canada. Policies and commitments related to the healthfulness of food environments within 6 action areas were assessed: 1) corporate nutrition strategy; 2) product (re)formulation; 3) nutrition information and labelling; 4) product and brand promotion; 5) product accessibility; and 6) disclosure of relationships with external organizations. Data were collected from publicly available sources, and companies were invited to supplement and validate information collected by the research team. Each company was then assigned a score out of 100 for each action area, and an overall BIA-Obesity score out of 100.

Results
Overall BIA-Obesity scores for manufacturers ranged from 18 to 75 out of 100 (median = 49), while scores for retailers ranged from 21 to 25 (median = 22). Scores were highest within the product (re)formulation (median = 60) followed by the corporate nutrition strategy (median = 59) domain for manufacturers, while retailers performed best within the corporate nutrition strategy (median = 53), followed by the disclosure of relationships with external organizations (median = 47) domain. Companies within both sectors performed worst within the product accessibility domain (medians = 8 and 0 for manufacturers and retailers, respectively).

Conclusions
This study highlights important limitations to self-regulatory approaches of the food and beverage industry to improve the healthfulness of food environments. Although some companies had specific, comprehensive, and transparent policies and commitments to address the healthfulness of food environments in Canada, most fell short of recommended best-practice. Additional mandatory government policies and regulations may be warranted to effectively transform Canadian food environments to promote healthier diets and prevent related non-communicable diseases.
Breaking the cycle of reoccurring low back pain with integrated motivational interviewing and cognitive behavioural therapy to facilitate education and exercise advice: a superiority randomised controlled trial study protocol
Authors: Watson Estelle D. , Marshall Paul W. , Morrison Natalie M. V. , Moloney Niamh , O’Halloran Paul , Rabey Martin , Niazi Imran Khan , Stevens Kirk , Kingsley Michael 
Published: September 2024

Abstract
Background
Non-specific low back pain is a common and costly global issue. Many people with low back pain live for years with ongoing symptom recurrence and disability, making it crucial to find effective prevention strategies. Motivational interviewing (MI) is an evidence-based patient-centred counselling style that helps motivate individuals to change their behaviours. In combination, MI and cognitive-behavioural therapy (MI-CBT) has the potential to yield long term improvements in pain and disability and reduce incidence of recurrence.

Method
This is a two-arm superiority randomised controlled trial comparing MI-CBT and Education (n = 83) with Education only (n = 83). Participants that have recovered from a recent episode of non-specific low back pain (7th consecutive day with pain ≤ 2 on a 0–10 numeric pain rating scale) will be eligible for inclusion into the study. Both groups will receive five 30-min sessions over a 10-week period as well as the Navigating Pain booklet, homework book and a standardised exercise programme. In the intervention group, MI-CBT techniques will be used to provide individualised support, identify beliefs, and increase engagement with the resources provided. Outcomes measures include pain (current and in the last 7 days) as rated on the numeric pain rating scale. This will be used to determine recurrence (number of participants who report back pain ≥ 3 out of 10 on the numeric pain rating scale). Furthermore, self-reported (1) pain intensity; (2) pain catastrophizing; (3) fear-avoidance beliefs; (4) pain self-efficacy; (5) depression and anxiety; (6) disability will be measured. All outcomes will be measured at baseline, and again at 3-, 6-, and 12-months post allocation.

Discussion
The effective delivery of self-management strategies to prevent recurrence of low back pain is an important aspect that requires urgent attention. This study will provide new information on the effectiveness of using an MI-CBT approach to facilitate self-management through education and exercise to improve low back pain outcomes. Evidence emerging from this trial has the potential to inform clinical practice and healthcare management of non-specific low back pain.

Trial registration
Prospectively registered with Australian New Zealand Clinical Trials Registry: ACTRN12623000746639 (10/07/2023).
Moderating effect of family structure on the relationship between early clinical exposure and emotional labor of nursing students: a cross-sectional study
Authors: Li Li , Xu Ruiyang , Wang Shan , Zhao Meng , Peng Sijing , Peng Xinning , Ye Qingyuan , Wu Chen , Wang Kefang 
Published: September 2024

Abstract
Background
Emotional labor is an essential component of nursing practice and is important for Generation Z nursing students born from the mid-1990s to early 2010s. They will become the backbone of the nursing workforce but present more emotional regulation problems. Studies on emotional labor are limited to clinical nurses and influencing factors at the individual level. The impacts of external systems on emotional labor of nursing students have not been explored. This study aimed to quantify the relationship between early clinical exposure and emotional labor and test the moderating effect of family structure on the relationship.

Methods
The cross-sectional study recruited 467 nursing students using convenience sampling from seven colleges and universities in mainland China. An e-survey created on WJX.CN was used to collect data in January 2023. Emotional labor (surface acting and deep acting) was measured with the Emotional Labor scale. Early clinical exposure (exposure or not and times of exposure) and family structure (nuclear family, extended family, and single-parent family) were assessed with self-reported questions. Descriptive statistics and the linear mixed-effects modeling were used to do the analyses.

Results
The mean scores of surface acting and deep acting were 26.66 ± 5.66 and 13.90 ± 2.40, respectively. A significant difference in scores of surface acting was not observed for exposure or not, whereas such a significant difference was found for times of exposure. Nursing students from extended families demonstrated significantly lower scores on surface acting while exposed to clinical practice compared with those from nuclear families. Family structure moderated the relationship between times of exposure and surface acting of nursing students when exposed to clinical practice for one time, but the significance disappeared when the times of exposure increased. No significant findings of early clinical exposure on deep acting were observed.

Conclusions
Early clinical exposure influenced emotional labor, and students from extended families were more likely to get benefits from early clinical exposure. Studies are needed to help students from nuclear families get comparable benefits on emotional labor as those from extended families, and improve deep acting by early clinical exposure.
Circulating microRNAs targeting coagulation and fibrinolysis in patients with severe COVID-19
Authors: Helin Tuukka A. , Lemponen Marja , Immonen Katariina , Lakkisto Päivi , Joutsi-Korhonen Lotta 
Published: September 2024

Abstract
Background
Coronavirus-19 disease (COVID-19) frequently causes coagulation disturbances. Data remains limited on the effects of microRNAs (miRNAs) on coagulation during COVID-19 infection. We aimed to analyze the comprehensive miRNA profile as well as coagulation markers and blood count in hospitalized COVID-19 patients.

Methods
Citrated plasma samples from 40 patients (24 men and 16 women) hospitalized for COVID-19 were analyzed. Basic coagulation tests, von Willebrand factor (VWF), ADAMTS13, blood count, C-reactive protein, and 27 miRNAs known to associate with thrombosis or platelet activation were analyzed. MiRNAs were analyzed using quantitative reverse transcription polymerase chain reaction (RT qPCR), with 10 healthy controls serving as a comparator.

Results
Among the patients, 15/36 (41%) had platelet count of over 360 × 109/L and 10/36 (28%) had low hemoglobin of < 100 g/L, while 26/37 (72%) had high VWF of over 200 IU/dL. Patients had higher levels of the miRNAs miR-27b-3p, miR-320a-3p, miR-320b-3p, and miR-424-5p, whereas levels of miR-103a-3p and miR-145-5p were lower than those in healthy controls. In total, 11 miRNAs were associated with platelet count. Let-7b-3p was associated with low hemoglobin levels of < 100 g/L. miR-24-3p, miR-27b-3p, miR-126-3p, miR-145-5p and miR-338-5p associated with high VWF.

Conclusion
COVID-19 patients differentially express miRNAs with target genes involved in fibrinolysis inhibition, coagulation activity, and increased inflammatory response. These findings support the notion that COVID-19 widely affects hemostasis, including platelets, coagulation and fibrinolysis.
Transcriptome dataset of Metroxylon sagu palms from multiple sago plantations in Sarawak
Authors: Pendi Fifi Hafizzah , Hussain Hasnain 
Published: September 2024

Abstract
Objective
Sago palm (Metroxylon sagu Rottb.) is one of the most important economic crops abundantly found in Mukah, Sarawak, Malaysia. The robustness of the palm triggered the Sarawak government’s selection as one of the state’s commodity crops, with the opening of several sago palm plantations. However, stunted (non-trunking) palms were reported in several sago palm plantations despite attaining a maturity period of more than ten years after cultivation. Research targeting this problem has been conducted in various fields, yet information on molecular mechanisms is still scarce. This study aimed to determine the genes responsible for sago palm’s normal phenotype (trunking) by attaining leaf transcriptomes from samples of all trunking sago palms from different sago palm plantations.

Data description
The conventional CTAB method was employed in the present investigation to extract total RNA from leaf tissues. Transcriptome sequencing was conducted on the Illumina NovaSeq 6000 platform. Differential expression analysis was performed using the DESeq2 package. A total of 6,119 differentially expressed genes, comprising 4,384 downregulated and 1,735 upregulated genes, were expressed in all three sago palm datasets. The datasets provide insights into the commonly expressed genes among trunking sago palms.