bluuebunny/crossref_metadata_2025_split huggingface dataset:
The CUT&RUN suspect list of problematic regions of the genome
Authors: Nordin Anna , Zambanini Gianluca , Pagella Pierfrancesco , Cantù Claudio 
Published: August 2023

Abstract
Background
Cleavage Under Targets and Release Using Nuclease (CUT&RUN) is an increasingly popular technique to map genome-wide binding profiles of histone modifications, transcription factors, and co-factors. The ENCODE project and others have compiled blacklists for ChIP-seq which have been widely adopted: these lists contain regions of high and unstructured signal, regardless of cell type or protein target, indicating that these are false positives. While CUT&RUN obtains similar results to ChIP-seq, its biochemistry and subsequent data analyses are different. We found that this results in a CUT&RUN-specific set of undesired high-signal regions.

Results
We compile suspect lists based on CUT&RUN data for the human and mouse genomes, identifying regions consistently called as peaks in negative controls. Using published CUT&RUN data from our and other labs, we show that the CUT&RUN suspect regions can persist even when peak calling is performed with SEACR or MACS2 against a negative control and after ENCODE blacklist removal. Moreover, we experimentally validate the CUT&RUN suspect lists by performing reiterative negative control experiments in which no specific protein is targeted, showing that they capture more than 80% of the peaks identified.

Conclusions
We propose that removing these problematic regions can substantially improve peak calling in CUT&RUN experiments, resulting in more reliable datasets.
Evaluation of interventions to prevent vasovagal reactions among whole blood donors: rationale and design of a large cluster randomised trial
Authors: McMahon Amy , Kaptoge Stephen , Walker Matthew , Mehenny Susan , Gilchrist Philippe T , Sambrook Jennifer , Akhtar Naim , Sweeting Michael , Wood Angela M , Stirrups Kathleen , Chung Ryan , Fahle Sarah , Johnson Elisha , Cullen Donna , Godfrey Rosemary , Duthie Shannon , Allen Louise , Harvey Paul , Berkson Michael , Allen Elizabeth , Watkins Nicholas A , Bradley John R , Kingston Nathalie , Miflin Gail , Armitage Jane , Roberts David J , Danesh John , Di Angelantonio Emanuele 
Published: August 2023

Abstract
Background
Vasovagal reactions (VVRs) are the most common acute complications of blood donation. Responsible for substantial morbidity, they also reduce the likelihood of repeated donations and are disruptive and costly for blood services. Although blood establishments worldwide have adopted different strategies to prevent VVRs (including water loading and applied muscle tension [AMT]), robust evidence is limited. The Strategies to Improve Donor Experiences (STRIDES) trial aims to reliably assess the impact of four different interventions to prevent VVRs among blood donors.

Methods
STRIDES is a cluster-randomised cross-over/stepped-wedge factorial trial of four interventions to reduce VVRs involving about 1.4 million whole blood donors enrolled from all 73 blood donation sites (mobile teams and donor centres) of National Health Service Blood and Transplant (NHSBT) in England. Each site (“cluster”) has been randomly allocated to receive one or more interventions during a 36-month period, using principles of cross-over, stepped-wedge and factorial trial design to assign the sequence of interventions. Each of the four interventions is compared to NHSBT’s current practices: (i) 500-ml isotonic drink before donation (vs current 500-ml plain water); (ii) 3-min rest on donation chair after donation (vs current 2 min); (iii) new modified AMT (vs current practice of AMT); and (iv) psychosocial intervention using preparatory materials (vs current practice of nothing). The primary outcome is the number of in-session VVRs with loss of consciousness (i.e. episodes involving loss of consciousness of any duration, with or without additional complications). Secondary outcomes include all in-session VVRs (i.e. with and without loss of consciousness), all delayed VVRs (i.e. those occurring after leaving the venue) and any in-session non-VVR adverse events or reactions.

Discussion
The STRIDES trial should yield novel information about interventions, singly and in combination, for the prevention of VVRs, with the aim of generating policy-shaping evidence to help inform blood services to improve donor health, donor experience, and service efficiency.

Trial registration
ISRCTN: 10412338. Registration date: October 24, 2019.
The recent introduction of Angiostrongylus cantonensis and its intermediate host Achatina fulica into Guadeloupe detected by phylogenetic analyses
Authors: Gamiette Gelixa , Ferdinand Séverine , Couvin David , Dard Céline , Talarmin Antoine 
Published: August 2023

Abstract
Background
Angiostrongylus cantonensis (rat lungworm) is the main pathogen responsible for eosinophilic meningitis in humans. One of its intermediate snail hosts, Achatina fulica, was already present in many countries around the world before it appeared in the West Indies in the late 1980s. In the French territories in the Caribbean and northern South America, the first cases of human neuroangiostrongyliasis were reported in Martinique, Guadeloupe and French Guiana in 2002, 2013 and 2017, respectively. In order to better characterize angiostrongyliasis in Guadeloupe, particularly its geographical origin and route of introduction, we undertook molecular characterization of adult worms of Angiostrongylus cantonensis and its intermediate host Achatina fulica.

Methods
Genomic DNA of adult Angiostrongylus cantonensis and Achatina fulica was extracted and amplified by polymerase chain reaction (PCR) targeting the mitochondrial genes cytochrome B and C for A. cantonensis and 16S ribosomal RNA for A. fulica. The PCR products were sequenced and studied by phylogenetic analysis.

Results
Cytochrome B and cytochrome C molecular markers indicate a monophyletic lineage of A. cantonensis adult worms in Guadeloupe. Two sequences of A. fulica were identified.

Conclusions
These results confirm the recent introduction of both Angiostrongylus cantonensis and Achatina fulica into Guadeloupe. Achatina fulica in Guadeloupe shares a common origin with those in Barbados and New Caledonia, while Angiostrongylus cantonensis in Guadeloupe shares a common origin with those in Brazil, Hawaii and Japan.

Graphical Abstract
The effects of alteration in muscle activation on the iliotibial band during an exhaustive run
Authors: Chen Shane Fei , Wang Yan , Bing Fangbo , Zhang Ming 
Published: August 2023

Abstract
Purpose
Long exhausted running causes pain at the lateral femoral epicondyle for some runners. The pain has been revealed to be related to the behavior of the iliotibial band (ITB) during running. The purpose of this study is to examine the effects of in-series musculature on the behavior of the ITB in healthy participants during an exhaustive run.

Methods
Twenty-five healthy participants (15 males, 10 females) were recruited in the current study. All participants performed a 30-minute exhaustive run at a self-selected speed with laboratory-provided footwear. Muscle activities of ITB-related muscles including tensor fascia latae (TFL), gluteus maximus (Gmax), gluteus medius (Gmed), biceps femoris (BF), and vastus lateralis (VL) were recorded using surface electromyography (EMG).

Results
Maximum amplitudes at the initial stage (the first minute), the mid stage (the 15-minute), and the end stage (the 30-minute) were compared during the exhaustive running. Significant decreases (p < 0.05) were observed in the maximum amplitudes of the TFL, Gmax, Gmed, and BF at the mid (decreased by ~ 15%) and end (decreased by ~ 30%) stages compared to the initial stage. The onset and the offset remained unaltered during the running (p ≥ 0.05).

Conclusion
The behavior of the healthy ITB might be altered due to the activities of the in-series musculature. Excessive compression forces might be applied to the lateral femoral epicondyle from the ITB to provide stability for the knee joint during an exhaustive run. The findings could provide a basic understanding of the behavior of healthy ITB.
On the basis of sex: male vs. female rat adenosine A1/A2A receptor affinity
Authors: Janse van Rensburg Helena D. , Terre’Blanche Gisella , Van der Walt Mietha M. 
Published: August 2023

Abstract
Objective
To ensure reproducibility in biomedical research, the biological variable sex must be reported; yet a reason for using male (instead of female) rodents is seldom given. In our search for novel adenosine receptor ligands, our research group routinely determines a test compound’s binding affinities at male Sprague-Dawley rat (r) adenosine A1 and A2A receptors via in vitro radioligand binding studies. This pilot study compared the binding affinities of four adenosine receptor ligands (frequently used as reference standards) at male and female adenosine rA1 and rA2A receptors.

Results
The inhibition constant (Ki) values determined using female rats correspond well to the values obtained using male rats and no markable difference could be observed in affinity and selectivity of reference standards. For example, DPCPX the selective adenosine A1 receptor antagonist: male rA1Ki: 0.5 ± 0.1 nM versus female rA1Ki: 0.5 ± 0.03 nM; male rA2AKi: 149 ± 23 nM versus female rA2AKi: 135 ± 29 nM. From the limited data at hand, we conclude that even when using female rats for in vitro studies without regard for the oestrous cycle, the obtained data did not vary much from their male counterparts.
Tumor-derived interleukin-1 receptor antagonist exhibits immunosuppressive functions and promotes pancreatic cancer
Authors: Fan Yu-Ching , Fong Yu-Cin , Kuo Chun-Tse , Li Chia-Wei , Chen Wei-Yu , Lin Jian-Da , Bürtin Florian , Linnebacher Michael , Bui Quoc Thang , Lee Kuan-Der , Tsai Yuan-Chin 
Published: August 2023

Abstract
Background
Pancreatic ductal adenocarcinoma (PDA) is a pernicious disease characterized by an immunosuppressive milieu that is unresponsive to current immunotherapies. Interleukin-1 receptor antagonist (IL-1Ra) is a natural anti-inflammatory cytokine; however, its contribution to cancer pathogenesis and immunosuppression remains elusive. In this research, we investigated the role and mechanism of IL-1Ra in malignant progression of PDA.

Results
Through analyzing clinical dataset and examining the pathological tumor tissues and serum samples, we have demonstrated that IL-1Ra expression is elevated in human PDA and positively associated with malignant progression of PDA. To study the biological function of IL-1Ra in tumors, we generated a set of mouse pancreatic cancer cell lines with a knockout (KO) of the Il1rn gene, encoding IL-1Ra, and compared the tumor growth rates in immune-competent and immune-deficient mice. We found that the Il1rn KO cells exhibited greater tumor inhibition in immune-competent mice, highlighting the crucial role of a functional immune system in Il1rn KO-mediated anti-tumor response. Consistently, we found an increase in CD8+ T cells and a decrease in CD11b+Ly6G− immunosuppressive mononuclear population in the tumor microenvironment of Il1rn KO-derived tumors. To monitor the inhibitory effects of IL-1Ra on immune cells, we utilized a luciferase-based reporter CD4+ T cell line and splenocytes, which were derived from transgenic mice expressing ovalbumin-specific T cell receptors in CD8+ T cells, and mice immunized with ovalbumin. We showed that IL-1Ra suppressed T cell receptor signaling and inhibited antigen-specific interferon-γ (IFN-γ) secretion and cytolytic activity in splenocytes.

Conclusions
Our findings illustrate the immunosuppressive properties of the natural anti-inflammatory cytokine IL-1Ra, and provide a rationale for considering IL-1Ra-targeted therapies in the treatment of PDA.
Experiences of a virtual day program for adolescents with eating disorders: a qualitative analysis of benefits and barriers
Authors: Catenacci Vanessa , Couturier Jennifer 
Published: August 2023

Abstract
Background
Throughout the COVID-19 pandemic, there was a detrimental impact to the symptoms and treatment of eating disorders, causing an increase in medical admissions and visits. Day treatment programs (DTPs), often used to bridge the gap between inpatient and outpatient treatment, were converted to online formats. This study aims to explore the impact of the transition to virtual DTPs on eating disorder treatment from the perspective of adolescents, their caregivers, and program staff.

Methods
Twelve participants (3 adolescents, 4 caregivers, 5 healthcare providers) in a virtual day treatment program were interviewed using a semi-structured interview guide. Interviews were transcribed and managed with qualitative software NVivo 11.0. Conventional analysis was used to inductively identify pertinent themes related to patient, caregiver, and healthcare staff perceptions and experiences of the virtual day treatment. Summative content analysis provided counts of the barriers and benefits of virtual day treatment as identified by participants.

Results
The majority of participants (10/12) had exposure to both virtual and in person settings, most participants (11/12) felt in-person day programs would be superior to virtual programs. Common limitations of the virtual format were feelings of isolation, less support from healthcare providers, parental burnout, and increased disordered eating. Common benefits were increased accessibility, parental involvement, improved communication with healthcare staff, and the ability for participants to be in their home environment and eat home food. Suggestions for improvement included designing a hybrid model of day treatment, increased family involvement, extending the day program to include dinners with family, and screening for patient appropriateness for the virtual setting.

Conclusion
This qualitative study suggests that there are many barriers to effective implementation of virtual day programs. However, the virtual DTP program offers increased accessibility to patients during a period of a health pandemic and to patients in rural/remote areas with limited treatment options. Suggestions provided by participants in this study, such as increased family involvement, frequency of in person check-ins and increased number of meals supported by the program, may help to improve outcomes in virtual day treatment programs.
Berberine-loaded albumin nanoparticles reverse aflatoxin B1-induced liver hyperplasia
Authors: Khedr Sarah M. , Ghareeb Doaa A. , Fathy Shadia A. , Hamdy Germine M. 
Published: August 2023

AbstractHepatocellular carcinoma (HCC) can be produced from aflatoxin B1 (AFB1) administration. Although berberine (BER) acts as an anticancer agent and can counteract the AFB1 effect, it has low bioavailability. Nanotechnology can overcome this problem. This research aimed to synthesize berberine nanoparticles (NPs) and then estimate their therapeutic effect compared to that of berberine against aflatoxin-induced hepatotoxicity. The desolvation method was used to prepare BER–NPs. Aflatoxicosis was induced by 5 consecutive intraperitoneal injections (IP) of 200 µg/kg/day AFB dissolved in dimethylsulfoxide (DMSO). After the induction period, two treatments were performed: the first with 100 mg/kg BER and the second with 10 mg/kg BER-NPs. Liver, kidney, and diabetic profiles were estimated by using standardized methods. Hepatic oxidative stress, inflammatory, cancer cell proliferation, and invasion markers were used by ELISA and qPCR techniques. The TEM image shows that both BSA NPs and BER-BSA NPs had spherical, regular, and uniform shapes. The BER encapsulation efficiency % was 78.5. The formed-BER-BSA NPs showed a loading capacity % of 7.71 and the synthesis yield % of 92.6. AFB1 increases pro-oxidant markers, decreases antioxidant systems, stimulates inflammatory enzymes, inhibits anti-inflammatory markers, decreases tumor suppressor enzymes, increases oncogenes, increases glycolytic activity, prevents cell death, and promotes cell growth. Most of the biochemical markers and hepatic architecture were normalized in the BER-BSA NP-treated group but not in the BER-treated group. Altogether, the obtained data proved that treatment with BER-NPs was more efficient than treatment with berberine against aflatoxicoses induced in rats.
But aren’t all soaps metal soaps? A review of applications, physico-chemical properties of metal soaps and their occurrence in cultural heritage studies
Authors: Russo Silvia , Brambilla Laura , Thomas Jean Baptiste , Joseph Edith 
Published: August 2023

Abstract
Metal soaps, the organic salts resulting from the interaction of fatty acids and metal cations, arouse interest in the scientific field because of their versatility in a great range of chemical applications as well as because of the mechanism of their formation during degradation processes. This article presents a review of the synthetic pathways used to produce metal soaps, their relevant physico-chemical properties, and how these reflect in their applications. Common industrial uses of metal soaps are reported, with a particular focus on those applications, such as cosmetics, paints, and coatings, that have an impact on the cultural heritage field. In addition, the occurrence of metal soaps in cultural heritage studies is presented, ranging from archaeological and ethnographic artefacts to fine art objects, and discussed per class of materials. An overview of the presence or absence of metal soaps in historical artefacts due to the interaction of metal parts or mineral pigments with fatty acids is given herein. This collection shows a variety of situations in which metal soaps—particularly lead, zinc and copper soaps—can form on composite objects made of different materials such as wood, leather and fatty-acid-containing materials (e.g., waxes), in the presence of metal, metal alloys or pigments.
PTS and PTSO, two organosulfur compounds from onion by-products as a novel solution for plant disease and pest management
Authors: Falcón-Piñeiro Ana , García-López David , Gil-Martínez Lidia , de la Torre José M. , Carmona-Yañez María Dolores , Katalayi-Muleli Antoine , Guillamón Enrique , Barrero-Domínguez Belén , López-Feria Silvia , Garrido Dolores , Baños Alberto 
Published: August 2023

AbstractBackgroundOver the past decade, the great impact of agricultural crop diseases has generated considerable economic losses and has compromised the production of edible crops at a time when the world population is only expected to rise, leading to the search for new pest management strategies. Besides that, the environmental impact resulting from the continued use of chemical pesticides has led to the search for natural and sustainable alternatives. One of the existing solutions that currently stands out for its effectiveness is the use of bioactive plant extracts. This study aims to evaluate the antimicrobial activity of propyl propane thiosulfinate (PTS) and propyl propane thiosulfonate (PTSO), two organosulfur compounds (OSCs) derived fromAllium cepa, against a wide range of target bacteria and fungi. To this end, various in vitro procedures were conducted as well as soil sanitization tests using sterile substrate inoculated with soil-borne pathogens. In addition, this study also evaluates the pesticidal activity of both compounds through in vitro mortality and repellence tests.ResultsPTS and PTSO revealed inhibition activity on all the pathogens tested, belonging to different taxonomic groups. Moreover, both significatively reduced the population of bacteria and fungi in soil. The quantification of active substances in soil carried out in parallel to the microbial quantification showed that their use reduces the risk of residue accumulation since they break down quickly when applied. The set of antimicrobial tests performed demonstrated that the antifungal effect of both compounds is higher than the bactericidal effect. Lastly, PTS and PTSO showed a concentration-dependent significant biocidal and repellent effect against aphids.ConclusionsThe results presented in this work demonstrate that both PTS and PTSO have a significant antimicrobial and pesticidal activity against the great majority of phytopathogens tested, being a promising tool to improve pest management in crops.Graphical Abstract
Ag+ colorimetric sensor based on graphene oxide/nano-platinum composite
Authors: Qu Yanping , Yakub Ibrahim , Baini Rubiyah , Hu WenShuo , Wang Lizhen 
Published: August 2023

AbstractWith the development of society, pollution accidents occur more frequently, and the effects of toxic substances containing silver on human health and environment are increasingly extensive. Therefore, the real-time on-site monitoring of silver ions is urgently needed. Based on the catalase-like properties of graphene/nano-platinum composites and the coupling effect between Pt and Ag+, a simple, unlabeled colorimetric sensing method is proposed to achieve the quantitative detection of Ag+. Under optimal conditions, the detection range of Ag+ by this colorimetric sensing method is 0.5–1000 μM, and the detection limit is 0.5 μM, which is lower than the previously reported detection limit of unlabeled Ag+ colorimetric sensing method, showing higher sensitivity and detection range. Under the same conditions, the sensor has almost no response to interference ions, showing good specific recognition ability. In addition, the colorimetric sensing method can be used to detect Ag+ in actual water samples, serving as a new paradigm for visual detection of Ag+.
Graphical abstract
Possible high risk of transmission of the Nipah virus in South and South East Asia: a review
Authors: Joshi Jagadish , Shah Yogendra , Pandey Kishor , Ojha Ram Prashad , Joshi Chet Raj , Bhatt Lok Raj , Dumre Shyam Prakash , Acharya Pushpa Raj , Joshi Hem Raj , Rimal Shikha , Shahi Ramesh , Pokharel Deepak , Khadka Kamal Singh , Dahal Bimal , Nepal Saroj , Dhami Ram Singh , Pant Krishna Prasad , Basnet Rajdip , Pandey Basu Dev 
Published: August 2023

AbstractNipah virus (NiV) is a zoonotic, single-stranded RNA virus from the family Paramyxoviridae, genus Henipavirus. NiV is a biosafety-level-4 pathogen that is mostly spread by Pteropus species, which serve as its natural reservoir host. NiV is one of the major public health challenges in South and South East Asia. However, few molecular studies have been conducted to characterise NiV in a specific region. The main objective of this review is to understand the epidemiology, pathogenesis, molecular surveillance, transmission dynamics, genetic diversity, reservoir host, clinical characteristics, and phylogenetics of NiV. South and South East Asian nations have experienced NiV outbreaks. Phylogenetic analysis confirmed that two primary clades of NiV are in circulation. In humans, NiV causes severe respiratory illness and/or deadly encephalitis. NiV is mainly diagnosed by ELISA along with PCR. Therefore, we recommend that the governments of the region support the One Health approach to reducing the risk of zoonotic disease transmission in their respective countries.