bluuebunny/crossref_metadata_2025_split huggingface dataset:
Lessons from the history ofAgave: ecological and cultural context for valuation of CAM
Authors: Davis Sarah C , Ortiz-Cano Hector G 
Published: June 2023

AbstractBackground and ScopeCrassulacean acid metabolism (CAM) is an intriguing physiological adaptation in plants that are widespread throughout many ecosystems. Despite the relatively recent mechanistic understanding of CAM in plant physiology, evidence from historical records suggests that ancient cultures in the Americas also recognized the value of CAM plants. Agave species, in particular, have a rich cultural legacy that provides a foundation for commercially valued products. Here, we review that legacy and potential relationships between ancient values and the needs of modern-day climate adaptation strategies.ConclusionsThere are many products that can be produced from Agave species, including food, sugar, fibre and medicines. Traditional knowledge about agricultural management and preparation of plant products can be combined with new ecophysiological knowledge and agronomic techniques to develop these resources in the borderland region of the southwestern USA and Mexico. Historical records of pre-Columbian practices in the Sonoran desert and remnants of centuries-old agriculture in Baja California and Sonora demonstrate the climate resilience of Agave agriculture. Commercial growth of both tequila and bacanora indicates the potential for large-scale production today, but also underscores the importance of adopting regenerative agricultural practices to accomplish environmentally sustainable production. Recent international recognition of the Appellation of Origin for several Agave species produced for spirits in Mexico might provide opportunities for agricultural diversification. In contrast, fibre is currently produced from several Agave species on many continents. Projections of growth with future climate change suggest that Agave spp. will be viable alternatives for commodity crops that suffer declines during drought and increased temperatures. Historical cultivation of Agave affirms that these CAM plants can supply sugar, soft and hard fibres, medicines and food supplements.
Functional characteristics of DNA N6-methyladenine modification based on long-read sequencing in pancreatic cancer
Authors: Zhou Dianshuang , Guo Shiwei , Wang Yangyang , Zhao Jiyun , Liu Honghao , Zhou Feiyang , Huang Yan , Gu Yue , Jin Gang , Zhang Yan 
Published: June 2023

Abstract
Abnormalities of DNA modifications are closely related to the pathogenesis and prognosis of pancreatic cancer. The development of third-generation sequencing technology has brought opportunities for the study of new epigenetic modification in cancer. Here, we screened the N6-methyladenine (6mA) and 5-methylcytosine (5mC) modification in pancreatic cancer based on Oxford Nanopore Technologies sequencing. The 6mA levels were lower compared with 5mC and upregulated in pancreatic cancer. We developed a novel method to define differentially methylated deficient region (DMDR), which overlapped 1319 protein-coding genes in pancreatic cancer. Genes screened by DMDRs were more significantly enriched in the cancer genes compared with the traditional differential methylation method (P &lt; 0.001 versus P = 0.21, hypergeometric test). We then identified a survival-related signature based on DMDRs (DMDRSig) that stratified patients into high- and low-risk groups. Functional enrichment analysis indicated that 891 genes were closely related to alternative splicing. Multi-omics data from the cancer genome atlas showed that these genes were frequently altered in cancer samples. Survival analysis indicated that seven genes with high expression (ADAM9, ADAM10, EPS8, FAM83A, FAM111B, LAMA3 and TES) were significantly associated with poor prognosis. In addition, the distinction for pancreatic cancer subtypes was determined using 46 subtype-specific genes and unsupervised clustering. Overall, our study is the first to explore the molecular characteristics of 6mA modifications in pancreatic cancer, indicating that 6mA has the potential to be a target for future clinical treatment.
CATAD: exploring topologically associating domains from an insight of core-attachment structure
Authors: Peng Xiaoqing , Li Yiming , Zou Mengxi , Kong Xiangyan , Sheng Yu 
Published: June 2023

Abstract
Identifying topologically associating domains (TADs), which are considered as the basic units of chromosome structure and function, can facilitate the exploration of the 3D-structure of chromosomes. Methods have been proposed to identify TADs by detecting the boundaries of TADs or identifying the closely interacted regions as TADs, while the possible inner structure of TADs is seldom investigated. In this study, we assume that a TAD is composed of a core and its surrounding attachments, and propose a method, named CATAD, to identify TADs based on the core-attachment structure model. In CATAD, the cores of TADs are identified based on the local density and cosine similarity, and the surrounding attachments are determined based on boundary insulation. CATAD was applied to the Hi-C data of two human cell lines and two mouse cell lines, and the results show that the boundaries of TADs identified by CATAD are significantly enriched by structural proteins, histone modifications, transcription start sites and enzymes. Furthermore, CATAD outperforms other methods in many cases, in terms of the average peak, boundary tagged ratio and fold change. In addition, CATAD is robust and rarely affected by the different resolutions of Hi-C matrices. Conclusively, identifying TADs based on the core-attachment structure is useful, which may inspire researchers to explore TADs from the angles of possible spatial structures and formation process.
SEMtree: tree-based structure learning methods with structural equation models
Authors: Grassi Mario , Tarantino Barbara 
Published: June 2023

AbstractMotivationWith the exponential growth of expression and protein–protein interaction (PPI) data, the identification of functional modules in PPI networks that show striking changes in molecular activity or phenotypic signatures becomes of particular interest to reveal process-specific information that is correlated with cellular or disease states. This requires both the identification of network nodes with reliability scores and the availability of an efficient technique to locate the network regions with the highest scores. In the literature, a number of heuristic methods have been suggested. We propose SEMtree(), a set of tree-based structure discovery algorithms, combining graph and statistically interpretable parameters together with a user-friendly R package based on structural equation models framework.ResultsCondition-specific changes from differential expression and gene–gene co-expression are recovered with statistical testing of node, directed edge, and directed path difference between groups. In the end, from a list of seed (i.e. disease) genes or gene P-values, the perturbed modules with undirected edges are generated with five state-of-the-art active subnetwork detection methods. The latter are supplied to causal additive trees based on Chu–Liu–Edmonds’ algorithm (Chow and Liu, Approximating discrete probability distributions with dependence trees. IEEE Trans Inform Theory 1968;14:462–7) in SEMtree() to be converted in directed trees. This conversion allows to compare the methods in terms of directed active subnetworks. We applied SEMtree() to both Coronavirus disease (COVID-19) RNA-seq dataset (GEO accession: GSE172114) and simulated datasets with various differential expression patterns. Compared to existing methods, SEMtree() is able to capture biologically relevant subnetworks with simple visualization of directed paths, good perturbation extraction, and classifier performance.Availability and implementationSEMtree() function is implemented in the R package SEMgraph, easily available at https://CRAN.R-project.org/package=SEMgraph.
Mitochondrial uncouplers impair human sperm motility without altering ATP content
Authors: Skinner Will M , Petersen Natalie T , Unger Bret , Tang Shaogeng , Tabarsi Emiliano , Lamm Julianna , Jalalian Liza , Smith James , Bertholet Ambre M , Xu Ke , Kirichok Yuriy , Lishko Polina V 
Published: June 2023

Abstract
In human spermatozoa, the electrochemical potentials across the mitochondrial and plasma membranes are related to sperm functionality and fertility, but the exact role of each potential has yet to be clarified. Impairing sperm mitochondrial function has been considered as an approach to creating male or unisex contraceptives, but it has yet to be shown whether this approach would ultimately block the ability of sperm to reach or fertilize an egg. To investigate whether the mitochondrial and plasma membrane potentials are necessary for sperm fertility, human sperm were treated with two small-molecule mitochondrial uncouplers (niclosamide ethanolamine and BAM15) that depolarize membranes by inducing passive proton flow, and evaluated the effects on a variety of sperm physiological processes. BAM15 specifically uncoupled human sperm mitochondria while niclosamide ethanolamine induced proton current in the plasma membrane in addition to depolarizing the mitochondria. In addition, both compounds significantly decreased sperm progressive motility with niclosamide ethanolamine having a more robust effect. However, these uncouplers did not reduce sperm adenosine triphosphate (ATP) content or impair other physiological processes, suggesting that human sperm can rely on glycolysis for ATP production if mitochondria are impaired. Thus, systemically delivered contraceptives that target sperm mitochondria to reduce their ATP production would likely need to be paired with sperm-specific glycolysis inhibitors. However, since niclosamide ethanolamine impairs sperm motility through an ATP-independent mechanism, and niclosamide is FDA approved and not absorbed through mucosal membranes, it could be a useful ingredient in on-demand, vaginally applied contraceptives.
British Society for Paediatric and Adolescent Dermatology assessment and support of mental health in children and young people with skin conditions: a multidisciplinary expert consensus statement and recommendations
Authors: McPherson Tess , Ravenscroft Jane , Ali Rukshana , Barlow Richard , Beattie Paula , Bewley Anthony , Bennett Sophie , Bleiker Tanya , Buckley Liz , Burgess Gary , Copperwheat Sarah  , Cunliffe Tim , Dejong Hannah , Fazel Mina , Heyman Isobel , Howard Emma  , Lambert Alice , Manktelow Claire , Moledina Zahra , Mohandas Padma , Moss Celia , Northover Guy , Paz Isabel , Proctor Andrew , Roxborough Christine , Shibib Shatha , Solman Lea , Srinivasan Jo , Wood Damian , Baron Susannah 
Published: June 2023

Abstract

Background
Psychological and mental health difficulties are common in children and young people (CYP) living with skin conditions and can have a profound impact on wellbeing. There is limited guidance on how best to assess and support the mental health of this population, who are at risk of poor health outcomes.

Objectives
To provide consensus-based recommendations on the assessment and monitoring of and support for mental health difficulties in CYP with skin conditions (affecting the skin, hair and nails); to address practical clinical implementation questions relating to consensus guidance; and to provide audit and research recommendations.

Methods
This set of recommendations was developed with reference to the AGREE II instrument. A systematic review and literature appraisal was carried out. A multidisciplinary consensus group was convened, with two virtual panel meetings held: an initial meeting to discuss the scope of the study, to review the current evidence and to identify areas for development; and a second meeting to agree on the content and wording of the recommendations. Recommendations were then circulated to stakeholders, following which amendments were made and agreed by email.

Results
The expert panel achieved consensus on 11 recommendations for healthcare workers managing CYP with skin conditions. A new patient-completed history-taking aid (‘You and Your Skin’) was developed and is being piloted.

Conclusions
The recommendations focus on improved mental health assessments for CYP presenting with a skin condition, with clinical guidance and suggested screening measures included. Information on accessing psychological support for CYP, when required, is given, and recommendations for staff training in mental health and neurodiversity provided. Embedding a psychosocial approach within services treating CYP with skin disease should ensure that CYP with psychological needs are able to be identified, listened to, supported and treated. This is likely to improve health outcomes.
Implementation of an Enhanced Recovery After Surgery (ERAS) Program in Colorectal Surgery: The Benefits of Late Adoption
Authors: Süsstrunk J , Mijnssen R , Müller-Stich B , Wilhelm A , Steinemann D 
Published: June 2023

Abstract

Background
Enhanced recovery after surgery (ERAS) protocols have shown beneficial outcomes in various surgical fields in the last 20 years. Nevertheless, some benefits such as lower complication rates, shorter length of stay and cost reduction might be related to other, simultaneously implemented technical improvements such as a minimally-invasive access or modified anesthesiology care.

Aims
To analyze the effects after the implementation of an ERAS protocol in 2021 in a high-volume colorectal center.

Methods
This is a propensity score matched single-center study comparing the short-term outcomes and cost analysis of patients undergoing elective colorectal surgery in an ERAS program from 2021 to August 2022 compared to regular perioperative care from 2019 to 2020.

Results
A total of 738 patients underwent elective colorectal surgery between 2019 and August 2022. 456 patients were included in the propensity score matched analysis with 228 patients per group (ERAS vs. non-ERAS). The predominant access in both groups was minimally-invasive with 78%; 17% were rectal procedures. There was no significant difference in age, sex, insurance status, body mass index, Charlson's Comorbidity Index, tumor entity and type of surgery between groups. Major complications (grade 3a or higher according to Clavien-Dindo) occurred in 6.6% vs. 7% (p=0.85) and anastomotic leakage demanding operative revision in 2.2% vs. 2.6% (p=0.68) in the ERAS and non-ERAS group, respectively. Mean length of stay (LOS) and mean costs per case were significantly lower in the ERAS group compared to the non-ERAS group (LOS 9.2 days vs. 12.7 days, p=0.001; costs 30’114 francs vs. 35’991 francs, p=0.004). At 30-day telephone follow-up, 97% of patients in the ERAS group were in a good general state and mean overall satisfaction level was at 9.2/10.

Conclusions
Late adoption to an ERAS protocol leads to a significant reduction of LOS and costs without increasing perioperative morbidity.
Breaking The Silence: A Content Analysis of Medical Students’ Perceptions of Failure in Medicine
Authors: Germann N , Lutz S , Beck J , Fourie L , Klasen J M 
Published: June 2023

Abstract

Background
Failure in medicine may cause severe harm to patients, especially in surgery where failure has immediate consequences. Despite often being an emotionally stressful experience for surgical residents, failure is a powerful teacher as well. Before entering residency where failure is inevitable, medical students should ideally learn how to talk about and cope with failure.

Aims
Educational interventions to support learners to regulate failure and its consequences are rare. Therefore, a four-day workshop entitled “How Physicians deal with Failure in Medicine” was offered to medical students at an academic institution to open the conversation about failure in medicine.

Methods
The curriculum provided insights into the ubiquity of failure in surgery and beyond. 30 participants wrote reflective essays as a pre- and post-intervention task. Tutors, namely two surgeons and a life coach, facilitated presentations, group discussions, and journal clubs about failure, and discussed potential coping strategies.

Results
The content analysis of 60 reflective essays revealed various self-experienced and observed failures in the clinical context. Experiencing and witnessing failure was emotionally draining and often in conflict with expectations of being a physician. Fear of failure was omnipresent, while students realized that failure in medicine is human and inevitable. Perceived clinical supervision often protected medical students from failure and its potential consequences. However, open communication about failure rarely occurred. Overall, medical students emphasized the importance of open conversations about failure to learn from it.

Conclusions
Medical students wish to discuss failure before entering residency. Without open discourse about failure, medical students, and later residents feel left alone with their experiences, triggering fear. Clinical supervisors should support learners entering clinical training by being more transparent about their own failures and sharing their coping strategies which will ultimately help them to make sense about failure experiences in order to learn from and cope with it.
Embosafe – A Novel Percutaneous Technique for Aorto-Iliac Thrombectomy without the Risk of Embolization
Authors: Mujagic E , D'amico R , Wolff T , Gürke L 
Published: June 2023

Abstract

Background
Aortoiliac thrombectomies have become more common during the Covid-19 pandemic. Classic surgical thrombectomy of the aorta and iliac arteries through an incision in the groin vessels harbours the risk of embolization to the viscero-renal as well as hypogastric arteries while percutaneous endovascular thrombectomy techniques can lead to peripheral embolization to the lower limb.

Aims
To describe a novel, percutaneous technique that tackles the above issues and to present our initial experience using it.

Methods
The principle of the technique is to percutaneously place large bore sheaths in the iliac arteries that deliberately occlude the latter to protect the lower limbs from embolization. Through one of these sheats, over the wire Fogarty® catheters can be placed and inflated in the ostia of the coeliac trunk, superior mesenteric artery, renal arteries and hypogastric arteries as needed. A large thrombectomy balloon catheter is then used to bring any aorto-iliac thrombus into the sheaths whereafter thrombus is removed from the sheaths by simply deflating their valves. Additional endovascular procedures of the aorto-iliac branches can be performed as needed.

Results
We report eight EmboSafe procedures in 7 patients (3 male, 4 female) with a median age of 61 (53-60). Sheaths were sized between 18F and 24F. Additional endovascular procedures had to be performed in 5 (62.5%) procedures, including relining of a renal briding stentgraft, thrombectomy of the coeliac trunk, kissing stentgrafts in the aortic bifurcation, thrombectomy of a hypogastric artery, one CERAB and stenting of a renal artery. All procedures were technically successful and all patients had palpable foot pulses on completion of the procedures. No patient had clinical signs of peripheral embolization.

Conclusions
EmboSafe is a very valid addition to the vascular surgeon's armamentarium when treating aorto-iliac thrombotic events because it is minimally invasive while still protecting against embolization and while offering the flexibility to perform additional endovascular procedures.
CD48 suppresses proliferation and migration as an immune-related prognostic signature in the cervical cancer immune microenvironment
Authors: Ma Yue , Yang Zhuo , Liu Jing , Wang Danbo 
Published: June 2023

Abstract
Cervical cancer (CC) is one of the most common malignant tumors in gynecology. Immunotherapy and targeted therapy are two particularly effective treatments. In this study, weighted gene co-expression network analysis and CIBERSORT algorithm that quantifies the composition of immune cells were used to analyze CC expression data based on the GEO database and identify modules related to T cells. Five candidate hub genes were identified by tumor-infiltrating immune cells estimation and Kaplan–Meier survival analysis according to CC data from The Cancer Genome Atlas (TCGA). Chemotherapeutic response, methylation, and gene mutation analyses were implemented so that the five candidate hub genes identified may be the potential biomarkers and therapeutic targets which were related to T cell infiltration. Moreover, the results of RT-qPCR revealed that CD48 was a tumor suppressor gene, which was negatively correlated with CC stages, lymph node metastasis, and differentiation. Furthermore, the functional study verified that the interference of CD48 was able to boost the proliferation and migration ability in vitro and the growth of transplanted tumors in vivo. Overall, we identified molecular targets related to immune infiltration and prognosis, regarded CD48 as a key molecule involved in the progression of CC, thus providing new insights into the development of molecular therapy and immunotherapeutics against CC.
Developmental differences in functional organization of multispectral networks
Authors: Petro Nathan M , Picci Giorgia , Embury Christine M , Ott Lauren R , Penhale Samantha H , Rempe Maggie P , Johnson Hallie J , Willett Madelyn P , Wang Yu-Ping , Stephen Julia M , Calhoun Vince D , Doucet Gaelle E , Wilson Tony W 
Published: June 2023

Abstract
Assessing brain connectivity during rest has become a widely used approach to identify changes in functional brain organization during development. Generally, previous works have demonstrated that brain activity shifts from more local to more distributed processing from childhood into adolescence. However, the majority of those works have been based on functional magnetic resonance imaging measures, whereas multispectral functional connectivity, as measured using magnetoencephalography (MEG), has been far less characterized. In our study, we examined spontaneous cortical activity during eyes-closed rest using MEG in 101 typically developing youth (9–15 years old; 51 females, 50 males). Multispectral MEG images were computed, and connectivity was estimated in the canonical delta, theta, alpha, beta, and gamma bands using the imaginary part of the phase coherence, which was computed between 200 brain regions defined by the Schaefer cortical atlas. Delta and alpha connectivity matrices formed more communities as a function of increasing age. Connectivity weights predominantly decreased with age in both frequency bands; delta-band differences largely implicated limbic cortical regions and alpha band differences in attention and cognitive networks. These results are consistent with previous work, indicating the functional organization of the brain becomes more segregated across development, and highlight spectral specificity across different canonical networks.
Platforming populism: the services transition, precarious urbanization, and digital platforms in the rise of illiberal populism in the Philippines
Authors: Cruz Jerik , de la Cruz Emille 
Published: June 2023

Abstract
Existing research on the adverse impact of digital platforms on democratic politics has generally focussed on supply side factors underlying illiberal populism. Yet by reinforcing a services-led growth model of capitalism in the developing world, the platform economy has also been implicated on the demand-side of the global populist upsurge by fostering new insecure classes as well as precarious urbanisation patterns. Through a case study of the rise of Rodrigo Duterte in the Philippines’ 2016 elections, we show how our theoretical argument has unfolded in one of the most well-known cases of illiberal populism within the Global South. Even while waging unprecedented disinformation campaigns on social media, the political opportunity structure underlying Duterte’s electoral victory in 2016 was fostered by the growth of ‘rising yet insecure’ classes linked to the Philippines’ services and platform economy, as well as the socio-spatial legacies of the country’s experience of premature deindustrialisation.