bluuebunny/crossref_metadata_2025_split huggingface dataset:
A novel and diverse group of Candidatus Patescibacteria from bathypelagic Lake Baikal revealed through long-read metagenomics
Authors: Haro-Moreno Jose M. , Cabello-Yeves Pedro J. , Garcillán-Barcia M. Pilar , Zakharenko Alexandra , Zemskaya Tamara I. , Rodriguez-Valera Francisco 
Published: February 2023

AbstractBackgroundLake Baikal, the world’s deepest freshwater lake, contains important numbers ofCandidatusPatescibacteria (formerly CPR) in its deepest reaches. However, previously obtained CPR metagenome-assembled genomes recruited very poorly indicating the potential of other groups being present. Here, we have applied for the first time a long-read (PacBio CCS) metagenomic approach to analyze in depth theCa.Patescibacteria living in the bathypelagic water column of Lake Baikal at 1600 m.ResultsThe retrieval of nearly complete 16S rRNA genes before assembly has allowed us to detect the presence of a novel and a likely endemic group ofCa.Patescibacteria inhabiting bathypelagic Lake Baikal. This novel group seems to possess extremely high intra-clade diversity, precluding complete genomes' assembly. However, read binning and scaffolding indicate that these microbes are similar to otherCa.Patescibacteria (i.e. parasites or symbionts), although they seem to carry more anabolic pathways, likely reflecting the extremely oligotrophic habitat they inhabit. The novel bins have not been found anywhere, but one of the groups appears in small amounts in an oligotrophic and deep alpine Lake Thun. We propose this novel group be named Baikalibacteria.ConclusionThe recovery of 16S rRNA genes via long-read metagenomics plus the use of long-read binning to uncover highly diverse “hidden” groups of prokaryotes are key strategies to move forward in ecogenomic microbiology. The novel group possesses enormous intraclade diversity akin to what happens withCa.Patescibacteria at the interclade level, which is remarkable in an environment that has changed little in the last 25 million years.
Protocol for a pilot randomised controlled trial to evaluate integrated support from pharmacist independent prescriber and third sector worker for people experiencing homelessness: the PHOENIx community pharmacy study
Authors: Paudyal Vibhu , Lowrie Richard , Mair Frances S. , Middleton Lee , Cheed Versha , Hislop Jennifer , Williamson Andrea , Barnes Nigel , Jolly Catherine , Saunders Karen , Allen Natalie , Jagpal Parbir , Provan George , Ross Steven , Hunter Carole , Tearne Sarah , McPherson Andrew , Heath Helena , Lombard Cian , Araf Adnan , Dixon Emily , Hatch Amy , Moir Jane , Akhtar Shabana 
Published: February 2023

Abstract

Background

People experiencing homelessness (PEH) have complex health and social care needs and most die in their early 40 s. PEH frequently use community pharmacies; however, evaluation of the delivery of structured, integrated, holistic health and social care intervention has not been previously undertaken in community pharmacies for PEH. PHOENIx (Pharmacy Homeless Outreach Engagement Non-medical Independent prescribing Rx) has been delivered and tested in Glasgow, Scotland, by NHS pharmacist independent prescribers and third sector homelessness support workers offering health and social care intervention in low threshold homeless drop-in venues, emergency accommodation and emergency departments, to PEH. Building on this work, this study aims to test recruitment, retention, intervention adherence and fidelity of community pharmacy-based PHOENIx intervention.

Methods
Randomised, multi-centre, open, parallel-group external pilot trial. A total of 100 PEH aged 18 years and over will be recruited from community pharmacies in Glasgow and Birmingham. PHOENIx intervention includes structured assessment in the community pharmacy of health, housing, benefits and activities, in addition to usual care, through weekly visits lasting up to six months. A primary outcome is whether to proceed to a definitive trial based on pre-specified progression criteria. Secondary outcomes include drug/alcohol treatment uptake and treatment retention; overdose rates; mortality and time to death; prison/criminal justice encounters; healthcare utilisation; housing tenure; patient-reported measures and intervention acceptability. Analysis will include descriptive statistics of recruitment and retention rates. Process evaluation will be conducted using Normalisation Process Theory. Health, social care and personal resource use data will be identified, measured and valued.

Discussion
If the findings of this pilot study suggest progression to a definitive trial, and if the definitive trial offers positive outcomes, it is intended that PHOENIx will be a publicly funded free-to-access service in community pharmacy for PEH. The study results will be shared with wider stakeholders and patients in addition to dissemination through medical journals and scientific conferences.

Trial registration
International Clinical Trial Registration ISRCTN88146807.
Approved protocol version 2.0 dated July 19, 2022.
Validation of a Thai semiquantitative food frequency questionnaire (semi-FFQ) for people at risk of metabolic syndrome
Authors: Nirdnoy Nattvara , Sranacharoenpong Kitti , Surawit Apinya , Pinsawas Bonggochpass , Mongkolsucharitkul Pichanun , Pongkunakorn Tanyaporn , Manosan Thamonwan , Ophakas Suphawan , Suta Sophida , Pumeiam Sureeporn , Mayurasakorn Korapat ,   Siriraj Health Study Group, Ratanasuwan Winai , Homsanit Mayuree , Charoencholvanich Keerati , Suktitipat Bhoom , Mitrpant Chalermchai , Pithukpakorn Manop , Suriyaphol Prapat , Krittayaphong Rungroj , Auewarakul Prasert , Tassaneetritap Boonrat , Poungvarin Naravat 
Published: February 2023

Abstract
Background
Food frequency questionnaires (FFQ) are a useful dietary assessment tool to determine relationships between diet and non-communicable diseases (NCDs). Our purpose was to validate a semiquantitative FFQ (semi-FFQ) for Thais at risk of metabolic syndrome (MS).

Methods
The researchers identified 345 men and women aged 30–65 years who were eligible for the study. Ninety-four participants were finally enrolled (54 in a “urine-collection not-required” group and 40 in a “urine collection” group). They were asked to maintain a 4-day food record for 4 weeks and partook in a semi-FFQ interview during week 4. Urine samples and biochemical results related to MS were collected. Validation results were associated with three primary nutrients for MS (sugar, fat, and sodium) and biochemical results (blood glucose, lipid profiles, blood pressure, and 24-h urine sodium).

Results
The biomarker level of each key MS nutrient significantly increased commensurate with rises in semi-FFQ estimated intakes. Correlation coefficients (r) were as follows: fasting blood glucose, r = 0.221 (fruits) and r = 0.229 (desserts); triglycerides, r = 0.112 (a la carte-dishes); low-density lipoprotein cholesterol, r = 0.205 (rice-with-topping dishes); systolic blood pressure, r = 0.272 (snacks) and r = 0.190 (a la carte dishes). Fasting blood glucose was a significant biomarker associated with the development of metabolic syndrome (OR 1.42, 95% CI 1.12–1.81). We also found that fat (OR 1.28, 95% CI 1.09–1.89), sodium (OR 1.98, 95% CI 1.05–1.95) and energy (OR 1.09, 95% CI 1.01–1.17) from an a la carte meal were significantly associated with the development of metabolic syndrome.

Conclusions
Thai food has a unique characteristic since it often pairs various ingredients and seasoning in one menu. This semi-FFQ is a tool that offers relatively valid ranking for intake of energy, nutrients, single foods, and mixed dishes based on Thai menus associated with a risk for developing metabolic syndrome and NCDs. Using this tool could help identify unhealthy dietary patterns and help develop recommendations for people at risk with the goal of preventing NCDs.
Identification of consensus hairpin loop structure among the negative sense subgenomic RNAs of SARS-CoV-2
Authors: Bokolia Naveen Prakash , Gadepalli Ravisekhar 
Published: February 2023

Abstract
Background
SARS-CoV-2 is the causative agent of worldwide pandemic disease coronavirus disease 19. SARS-CoV-2 bears positive sense RNA genome that has organized and complex pattern of replication/transcription process including the generation of subgenomic RNAs. Transcription regulatory sequences have important role in the pausing of replication/transcription and generation of subgenomic RNAs.

Results
In the present bioinformatics analysis, a consensus secondary structure was identified among negative sense subgenomic RNAs of SARS-CoV-2. This consensus region is present at the adjacent of initiation codon.

Conclusions
This study proposed that consensus structured domain could involve in mediating the long pausing of replication/transcription complex and responsible for subgenomic RNA production.
rs3761548 (C/A) and rs5902434 (del/ATT) polymorphisms of Foxp3 gene in Iranian patients with migraine
Authors: Faraji Fardin , Mosayebi Ghasem , Bahrami Maryam , Shojapour Mana 
Published: February 2023

Abstract
Background
Migraine is a neurovascular disorder; several studies have demonstrated the immune system plays a key role in migraine pathogenesis. The aim of this study was to investigate the association between FOXP3 gene polymorphism and susceptibility to migraine.

Methods
In a case–control study, 55 whole blood samples of patients with migraine and 80 healthy samples were collected. After DNA extraction, genotyping of the rs5902434 (del/ATT) and rs3761548 (C/A) FOXP3 was performed using sequence-specific primers method (PCR-SSP).

Results
The results of this study showed that there were statistically significant differences between patient and control group in genotype frequencies of rs3761548. In addition, the frequency of heterozygous genotype AC at rs3761548 in patients was found to be significantly higher than controls. We also found no significant differences between cases and controls were found in the allelic and genotype distribution of the rs5902434 (del/ATT) polymorphism. None of the rs5902434 (del/ATT) genotypes showed any significant association with the migraine.

Conclusions
According to finding of our study, polymorphism rs3761548 in FOXP3 gene were associated with susceptibility to migraine. Further studies with larger sample sizes and different populations in other parts of the world are needed to investigate relationship between this polymorphism on migraine susceptibility.
Role of arterial spin labeling magnetic resonance perfusion in acute ischemic stroke
Authors: ElBeheiry Ahmed Adel , Hanora Mohamed Ahmed , Youssef Ahmed Farid , Al Neikedy Abdel Aziz Mohamed , Elhabashy AbdelRahman , Khater Hamada Mohamed 
Published: February 2023

AbstractBackgroundArterial spin labeling (ASL) is a recently used magnetic resonance imaging (MRI) perfusion technique in acute cerebrovascular stroke conditions; it can detect the hypo perfused areas on basis of qualitative and quantitative measurements and also identify the area at risk known as penumbra by detecting the diffusion/perfusion mismatch. The purpose of this study was to assess the role of ASL perfusion technique in management of acute ischemic stroke and its ability to predict the clinical outcome of acute stroke patients. The study was prospectively carried out on 33 patients clinically presented with acute stroke from the first of August 2020 till the first of August 2021. All cases were clinically assessed by stroke consultant followed by brain imaging including conventional MRI and ASL perfusion technique, based upon which management was established. These imaging data were correlated with the clinical outcome after 3 months using Modified Rankin Scale.ResultsSixteen cases (48.48%) showed ischemic penumbra with diffusion perfusion mismatch with three cases presenting within the first 4 h managed by intravenous thrombolytic therapy and 13 cases presenting later than 4 h, 10 of whom were managed by endovascular intervention. The group with ischemic penumbra showed significant positive correlation with favorable clinical outcome while the group without ischemic penumbra showed significant positive correlation with poor clinical outcome. Quantitative ASL values were statistically significantly higher (p ≤ 0.05) in patients with favorable clinical outcome than those with poor clinical outcome. The estimated cut off values of ASL absolute cerebral blood flow and relative cerebral blood flow to predict favorable or poor outcome using ROC curve analysis were 19 ml/100gm/min and 74% compared to the contralateral side respectively.ConclusionThe use of MRI as a primary diagnostic tool in arterial ischemic stroke with the application of non-contrast ASL perfusion sequence allows precise detection of perfusion deficit and diffusion perfusion mismatch (penumbra) and provides a reliable insight into outcome prediction.
A deep reinforcement learning model for resilient road network recovery under earthquake or flooding hazards
Authors: Fan Xudong , Zhang Xijin , Wang Xiaowei , Yu Xiong 
Published: February 2023

AbstractAs the backbone and the ‘blood vessel’ of modern cities, road networks provide critical support for community activities and economic growth, with their roles even more crucial due to the dramatic progress in urbanization. The service of road networks is subjected to the increasing frequency of high-consequence natural hazards such as earthquakes, floods, hurricanes, etc. Identifying resilient restoration sequences is essential to mitigate the disruption of such important infrastructure networks. This paper investigates a novel decision-support model to optimize post-disaster road network repair sequence. The model, named as GCN-DRL model, integrates the advantages of deep reinforced learning (DRL) with graph convolutional neural network (GCN), two emerging artificial intelligence (AI) techniques to achieve efficient recovery of road network service. The model is applied to analyze two cases of community road networks in the US that are subjected to different types of hazards, i.e., earthquakes and flooding. The performance of repair sequence by the GCN-DRL model is compared with two commonly used methods, i.e., repair sequence by the genetic algorithm and by prioritization based on graph importance with betweenness centrality. The results showed the decision sequence by GCN-DRL model consistently achieved superior performance in road network restoration than the conventional methods. The AI-based decision model also features high computational efficiency since the GCN-DRL model can be trained before the hazard. With a pre-trained GCN-DRL model, a close to optimal decision-making process can be made available rapidly for different types of new hazards, which is advantageous in efficiently responding to hazards when they happen. This study demonstrates the promise of a new AI-based decision support model to improve the resilience of road networks by enabling efficient post-hazards recovery.
The impact of screen exposure among school-aged children in South India during the COVID-19 pandemic: an online survey
Authors: Dessai Teja Deepak , Sigdel Surakshya , Chand Thakendra , Bhat Rashmi J. , Kumar Kaushlendra 
Published: February 2023

Abstract
Background
The impact of excessive screen time with personal listening devices (PLDs) on vision, hearing, balance, and overall health among adults has been reported in the literature. However, its impact on children is not well documented. A survey was undertaken to highlight the possible effects of screen time combined with transducers on vision, hearing, balance, and overall health complaints in children via parental proxy. This cross-sectional survey consisted of questions divided into four domains: vision, hearing, balance, and overall health. It was conducted online using social media to avail total maximum responses.

Results
A total of 136 responses were obtained from the parents of children studying from grade 1 to 8 through the survey conducted in south India. Increased negative impact on vision was observed in more than 50% of children. Similarly, the hearing and balance domain reported 16% ear pain, 4.4% tinnitus, 9.6% dizziness, 8.8% nausea, and 2.2% imbalance while walking. Likewise, the overall stress domain reported 26.5% general body discomfort, 37.5% neck pain and stiffness, 29.4% headaches, 43.4% lack of concentration, 39.7% overall changes in child’s health and 46.3% behavioral issues with various severity markings (slight to severe).

Conclusions
Longer periods of screen exposure have various negative impacts on vision, hearing, balance system, and overall health. These effects have to be managed for the health of our children.
BXQ-350: Modulating ceramide and sphingosine-1-phosphate for antitumor activity in patients with advanced CRC.
Authors: Rixe Olivier , Curry Richard Charles , Morris John Charles , Muller Carolyn , Noonan Anne M. , Puduvalli Vinay K. , Villano John L. , Wise-Draper Trisha Michel , Wesolowski Robert , Yilmaz Emrullah , Tapolsky Gilles , Takigiku Ray 
Published: February 2023

154 Background: Sphingolipids are a class of bioactive signaling molecules implicated in multiple cellular processes and molecular pathways. Many publications have demonstrated that ceramides are proapoptotic, synergize with cancer treatments, and mitigate chemoresistance. Findings also demonstrated that sphingosine-1-phosphate (S1P) is a key sphingolipid that promotes cancer cell proliferation, activates multiple oncogenic pathways, and stimulates immuno-suppressor cell populations promoting a pro-tumoral microenvironment. Several studies of colorectal cancer patients have shown high levels of ceramides being associated with improved survival, while high S1P levels are associated with a poor prognosis. Hence, modulation of sphingolipid metabolism continues to be a promising treatment approach. Methods: BXQ-350 is a nanovesicle of Saposin C, an allosteric activator of sphingolipid metabolism, that lowers systemic S1P and increases C18 ceramide. BXQ-350 was investigated in a Phase 1 dose-escalation safety study in an all-comer cancer patients with advanced solid malignancies ( NCT02859857 ) to determine its safety profile and potential clinical activity as monotherapy. Samples were collected to explore potential biomarkers. Results: 13 patients (~17.8% of evaluable patients) had a clinical benefit up to cycle 6 (PR, SD), with the majority experiencing a decrease in systemic S1P levels and an increase in C18 levels. 8 patients (~11% of evaluable patients) had PFS > 6 months, with 2 patients still on study six years after enrollment. Analysis of plasma samples also revealed an increase in anti-tumoral cytokines (IFNg, TNFa, IL-2) and a decrease in pro-tumoral ones (IL-6, 8, 10). Among patients with PFS > 6 months, there were 4 recurrent CRC patients (1PR, 3SD): 1 patient had a PFS of ~12 months, 2 of ~18 months, and 1 is still on study after 6 years. Conclusions: Results of this Phase 1 study in heavily pretreated patients show BXQ-350 was well tolerated and seem to generate a clinical benefit in CRC patients via modulation of S1P and ceramides. A phase 2 trial of BXQ-350 in combination with FOLFOX/Bevacizumab in newly diagnosed mCRC is on-going with plans to further investigate this novel mechanism of action. Clinical trial information: 02859857 .
BXQ-350 may alleviate symptoms of chemotherapy- induced peripheral neuropathy via modulation of S1P.
Authors: Wesolowski Robert , Noonan Anne M. , Curry Richard Charles , Morris John Charles , Muller Carolyn , Puduvalli Vinay K. , Rixe Olivier , Villano John L. , Wise-Draper Trisha Michel , Yilmaz Emrullah , Tapolsky Gilles , Takigiku Ray 
Published: February 2023

93 Background: Chemotherapy Induced Peripheral Neuropathy (CIPN) is a debilitating side effect associated with many chemotherapeutic agents. It significantly impacts quality of life during treatment, causes lasting neuropathy, and may also shorten the treatment regimen, potentially impacting clinical benefit. The pathology of CIPN is still not completely understood, however, increasing evidence suggests sphingosine-1-phosphate (S1P) may be an important signaling molecule. Altered neuronal sphingolipid metabolism has been linked to neuropathic pain, evidenced by elevated plasma levels of S1P in patients receiving chemotherapy. Methods: BXQ-350 is a nanovesicle of Saposin C, an allosteric activator of sphingolipid metabolism, that lowers systemic S1P. BXQ-350 was investigated in an adult Phase 1 dose-escalation safety study in heavily pretreated all-comer cancer patients with advanced solid malignancies ( NCT02859857 ). The primary objective was to determine the safety profile and potential clinical activity of BXQ-350 as monotherapy. Samples were collected to explore potential biomarkers. Results: BXQ-350 was safe and well tolerated. Clinical signs of activity were observed in 13 patients (~17.8% of evaluable patients) experiencing a clinical benefit (PR, SD) up to cycle 6 and beyond including: 4 CRC, 1 pancreatic, and 1 GIST patient. Two patients are still on study six years after enrollment, including 1 CRC. Interestingly, a pancreatic cancer patient with chronic CIPN at time of enrollment spontaneously reported a significant improvement of her neuropathic symptoms shortly after receiving BXQ-350. Investigation of potential improvements in patients with chronic CIPN at time of enrollment revealed that 4 out of 10 patients experienced an improvement of their symptoms that seemed to be associated with a decrease in S1P systemic levels following BXQ-350 administration. BXQ-350 was subsequently investigated in a murine oxaliplatin-CIPN preclinical model with results showing a dose-dependent prevention/resolution of CIPN correlating with decreasing systemic S1P levels. Conclusions: Results of this Phase 1 study in heavily pretreated patients shows that BXQ-350 was well tolerated and seems to generate a clinical benefit via modulation of S1P. There were preliminary signs that BXQ-350 may alleviate symptoms of CIPN in relation to decreasing S1P concentration. Additional studies are underway to better understand this novel mechanism of action. Clinical trial information: 02859857 .