bluuebunny/crossref_metadata_2025_split huggingface dataset:
NT-seq: a chemical-based sequencing method for genomic methylome profiling
Authors: Li Xuwen , Guo Shiyuan , Cui Yan , Zhang Zijian , Luo Xinlong , Angelova Margarita T. , Landweber Laura F. , Wang Yinsheng , Wu Tao P. 
Published: May 2022

AbstractDNA methylation plays vital roles in both prokaryotes and eukaryotes. There are three forms of DNA methylation in prokaryotes:N6-methyladenine (6mA),N4-methylcytosine (4mC), and 5-methylcytosine (5mC). Although many sequencing methods have been developed to sequence specific types of methylation, few technologies can be used for efficiently mapping multiple types of methylation. Here, we present NT-seq for mapping all three types of methylation simultaneously. NT-seq reliably detects all known methylation motifs in two bacterial genomes and can be used for identifying de novo methylation motifs. NT-seq provides a simple and efficient solution for detecting multiple types of DNA methylation.
Physico-analytical studies on some heterocyclic azo dyes and their metal complexes with some transition metals
Authors: El-Seify Fathy A. , Azab Hassan A. , Degedy Fikrea S. , Abdel-Mageed Khalid A. , El-Dossoki Farid I. 
Published: May 2022

AbstractIn this investigation, the azo dyes; 2-(3′-phenyl-5′-pyrazolyl azo) schaffer acid (la) and 2-(3′-phenyl-5′-pyrazolyl azo) resorcinol (Ib); were prepared through diazotizing 3-phenyl-5-aminopyrazole (PAP) and coupling the resulting diazonium salt with Schäffer acid and resorcinol respectively. The prepared azo dyes are characterized using both IR spectra and the elemental analysis (C, H, N and S). The prepared azo dyes are used as chromogenic reagents for the spectrophotometric determination of copper (II), nickel (II), cobalt (II) and zinc (II) ions. The conditional acid dissociation constants of these azo dyes (la and Ib) and the stability constants of its metal ion complexes have been determined by spectro-analytical methods. The effect of pH, time, organic solvent and the foreign ions on the spectrophotometric determination of these ions and their complexes with the azo dyes under study were studied. The stoichiometric ratio (M:L) of the formed complexes was also determined. The molar absorptivity, the Sandell's sensitivity values, the obeyance of Beers law and the stability constants of the formed complexes have been also determined and discussed.
Comprehensive genomic and tumour immune profiling reveals potential therapeutic targets in malignant pleural mesothelioma
Authors: Creaney Jenette , Patch Ann-Marie , Addala Venkateswar , Sneddon Sophie A. , Nones Katia , Dick Ian M. , Lee Y. C. Gary , Newell Felicity , Rouse Ebony J. , Naeini Marjan M. , Kondrashova Olga , Lakis Vanessa , Nakas Apostolos , Waller David , Sharkey Annabel , Mukhopadhyay Pamela , Kazakoff Stephen H. , Koufariotis Lambros T. , Davidson Aimee L. , Ramarao-Milne Priya , Holmes Oliver , Xu Qinying , Leonard Conrad , Wood Scott , Grimmond Sean M. , Bueno Raphael , Fennell Dean A. , Pearson John V. , Robinson Bruce W. , Waddell Nicola 
Published: May 2022

Abstract
Background
Malignant pleural mesothelioma (MPM) has a poor overall survival with few treatment options. Whole genome sequencing (WGS) combined with the immune features of MPM offers the prospect of identifying changes that could inform future clinical trials.

Methods
We analysed somatic mutations from 229 MPM samples, including previously published data and 58 samples that had undergone WGS within this study. This was combined with RNA-seq analysis to characterize the tumour immune environment.

Results
The comprehensive genome analysis identified 12 driver genes, including new candidate genes. Whole genome doubling was a frequent event that correlated with shorter survival. Mutational signature analysis revealed SBS5/40 were dominant in 93% of samples, and defects in homologous recombination repair were infrequent in our cohort. The tumour immune environment contained high M2 macrophage infiltrate linked with MMP2, MMP14, TGFB1 and CCL2 expression, representing an immune suppressive environment. The expression of TGFB1 was associated with overall survival. A small subset of samples (less than 10%) had a higher proportion of CD8 T cells and a high cytolytic score, suggesting a ‘hot’ immune environment independent of the somatic mutations.

Conclusions
We propose accounting for genomic and immune microenvironment status may influence therapeutic planning in the future.
Climate change-induced background tree mortality is exacerbated towards the warm limits of the species ranges
Authors: Taccoen Adrien , Piedallu Christian , Seynave Ingrid , Gégout-Petit Anne , Gégout Jean-Claude 
Published: May 2022

Abstract
Key message
An influence of the recent changes in temperature or rainfall was demonstrated, increasing background tree mortality rates for 2/3 of the 12 studied tree species. Climate change-induced tree mortality was exacerbated towards the warm or dry limits of the species ranges, suggesting in these areas a progressive replacement by more xeric species.

Context
Despite the identification of climate change effects on tree mortality in various biomes, the characterization of species-specific areas of vulnerability remains poorly understood.

Aims
We sought to assess if the effects of temperature and rainfall changes on background tree mortality rates, which did not result from abrupt disturbances, were linked to climate change intensity only, or if they also depended on the tree’s location along climatic gradients.

Methods
We modelled background mortality for 12 of the most common European tree species using 265,056 trees including 4384 dead trees from the French national forest inventory. To explain mortality, we considered variables linked to tree characteristics, stand attributes, logging intensity and site environmental characteristics, and climate change effects.

Results
We found an influence of temperature and rainfall changes on 9 species out of 12. For 8 of them, climate change-induced tree mortality was exacerbated towards the warm or dry limits of the species ranges.

Conclusion
These results highlight that tree mortality varies according to the climate change intensity and the tree location along temperature and rainfall gradients. They strengthen the poleward and upward shifts of trees forecasted from climate envelope models for a large number of European tree species.
Mental health and psychological wellbeing of maritime personnel: a systematic review
Authors: Brooks Samantha K. , Greenberg Neil 
Published: May 2022

AbstractBackgroundSeafaring has frequently been reported to be a ‘risky occupation’ in terms of both physical and mental health. Individuals working in seafaring professions are exposed to various stressors in the workplace, including social isolation, exposure to poor physical conditions and long work hours. This systematic review aimed to update previous reviews by collating recent literature (published between 2012 and 2021) on the factors associated with mental health and wellbeing in seafaring personnel.MethodsFour electronic databases were searched in April 2021 for primary peer-reviewed studies on factors associated with the mental health and psychological wellbeing of seafarers or interventions to improve the wellbeing of seafarers, published in English in or after the year 2012. Thematic analysis was used to synthesise the data and standardised measures of quality appraisal were used to assess risk of bias.ResultsSixty-three studies were reviewed. Risk factors for poor mental health among seafarers appear to be younger age; being single; poor physical health; exposure to noise/vibration; feeling unsafe; high job demands; long working hours; night/irregular shifts; poor sleep; poor team cohesion; poor perception of management; poor social support; lack of autonomy; scheduling uncertainties; long duration at sea; and over-commitment.ConclusionsThere are numerous steps that maritime managers could take to improve the wellbeing of their personnel, including increased monitoring of the potential for poor mental health in their staff, increasing crew numbers and provision of education and support.
PROTEUS: an immersive tool for exploring the world of cultural heritage across space and time scales
Authors: Albertini Niccolò , Baldini Jacopo , Dal Pino Andrea , Lazzari Federico , Legnaioli Stefano , Barone Vincenzo 
Published: May 2022

Abstract
In the field of digital humanities, it is increasingly necessary to develop and validate virtual reality tools that are capable of combining various scientific data in a virtualized context providing also access and user friendly consultation of online repositories. This paper reports the main aspects of the implementation of a virtual reality tool integrated with an online repository for storing 3D models, metadata and chemical analyses related to different sectors of digital humanities. The virtual reality software, developed for the Oculus Quest 2 hardware, is called PROTEUS and allows for seamless transition from the macroscopic world of digital humanities to the microscopic world of molecular sciences. The paper illustrates, by means of some case studies, the performances of this innovative tool that permits the researcher to understand and manipulate objects, to test hypotheses and to seek meaningful results, visualising the metadata while changing the parameters of the simulation in a dynamic and interactive way. This represents also a significant step forward in the democratisation of science, thanks to an user-friendly and immersive access to advanced scientific algorithms, which allow the natural perception of structural and topological features of the underlying molecular and supra-molecular systems.

Graphical Abstract
Differential regional perfusion of the human anterior cruciate ligament: quantitative magnetic resonance imaging assessment
Authors: Lin Kenneth M. , Vermeijden Harmen D. , Klinger Craig E. , Lazaro Lionel E. , Rodeo Scott A. , Dyke Jonathan P. , Helfet David L. , DiFelice Gregory S. 
Published: May 2022

Abstract
Purpose
Surgical reconstruction is the current standard for ACL rupture treatment in active individuals. Recently, there is renewed interest in primary repair of proximal ACL tears. Despite this, ACL biology and healing potential are currently not well understood. Vascularity is paramount in ACL healing; however, previous ACL vascularity studies have been limited to qualitative histological and dissection-based techniques. The study objective was to use contrast-enhanced quantitative-MRI to compare relative perfusion of proximal, middle, and distal thirds of the in situ ACL. We hypothesized perfusion would be greatest in the proximal third.

Methods
Fourteen cadaveric knees were studied (8 females, 6 males), age 25–61 years. Superficial femoral, anterior tibial, and posterior tibial arteries were cannulated; without intraarticular dissection. Contrast-enhanced quantitative-MRI was performed using a previously established protocol. ACL regions corresponding to proximal, middle, and distal thirds were identified on sagittal-oblique pre-contrast images. Signal enhancement (normalized to tibial plateau cartilage) was quantified to represent regional perfusion as a percentage of total ACL perfusion. Comparative statistics were computed using repeated measures ANOVA, and pairwise comparisons performed using the Bonferroni method.

Results
Relative perfusion to proximal, middle, and distal ACL zones were 56.0% ±17.4%, 28.2% ±14.6%, and 15.8% ±16.3%, respectively (p = 0.002). Relative perfusion to the proximal third was significantly greater than middle (p = 0.007) and distal (p = 0.001). No statistically relevant difference in relative perfusion was found to middle and distal thirds (p = 0.281). Post-hoc subgroup analysis demonstrated greater proximal perfusion in males (66.9% ± 17.3%) than females (47.8% ± 13.0%), p = 0.036.

Conclusion
Using quantitative-MRI, in situ adult ACL demonstrated greatest relative perfusion to the proximal third, nearly 2 times greater than the middle third and 3 times greater than the distal third. Knowledge of differential ACL vascular supply is important for understanding pathogenesis of ACL injury and the process of biological healing following various forms of surgical treatment.
Strangulated small bowel obstruction caused by isolated obturator nerve and pelvic vessels after pelvic lymphadenectomy in gynecologic surgery: two case reports
Authors: Ideyama Riko , Okuchi Yoshihisa , Kawada Kenji , Itatani Yoshiro , Mizuno Rei , Hida Koya , Obama Kazutaka 
Published: May 2022

Abstract
Background
Although small bowel obstruction (SBO) is a major complication occurring after abdominal surgery, few reports have described strangulated SBO after pelvic lymphadenectomy (PL). This report describes two cases of strangulated SBO caused by a skeletonized obturator nerve and pelvic vessels after laparoscopic PL during gynecologic surgery.

Case presentation
Case 1: A 57-year-old woman with endometrial cancer underwent a laparoscopic semi-radical total hysterectomy with PL. Nine months after the operation, she visited our emergency room complaining about subacute pain spreading in the right groin, right buttock, and dorsal part of the right thigh. She had no abdominal pain. Although her symptoms were not typical, computed tomography (CT) revealed strangulated SBO in the right pelvis. Laparoscopic surgery revealed that the small bowel was ischemic. Then we converted to open surgery. We transected the right obturator nerve and umbilical artery, which constructed an internal hernia orifice in the right pelvis, followed by resection of the ischemic small bowel. Fortunately, during 6-month follow-up, she showed only slight difficulty in walking as a postoperative complication. Case 2: A 62-year-old woman with cervical cancer underwent laparoscopic radical hysterectomy with PL. Six months after the operation, she visited our hospital emergently because of sudden onset of abdominal pain and vomiting. CT showed strangulated SBO. Urgent laparoscopic surgery exhibited the incarcerated small bowel at the right pelvis. Consequently, we converted to open surgery. The terminal ileum was detained into the space constructed by the right umbilical artery. We cut the umbilical artery and performed ileocecal resection. After the surgery, she was discharged with no complication or sequela.

Conclusion
When examining a patient after PL who complains of severe pain or symptoms, one should consider the possibility of PL-related SBO, even if the pain is apparently atypical for SBO.
Gait rehabilitation for foot and ankle impairments in early rheumatoid arthritis: a feasibility study of a new gait rehabilitation programme (GREAT Strides)
Authors: Hendry Gordon J. , Bearne Lindsay , Foster Nadine E. , Godfrey Emma , Hider Samantha , Jolly Lisa , Mason Helen , McConnachie Alex , McInnes Iain B. , Patience Aimie , Sackley Catherine , Sekhon Mandeep , Stanley Bethany , van der Leeden Marike , Williams Anita E. , Woodburn Jim , Steultjens Martijn P. M. 
Published: May 2022

AbstractBackgroundFoot impairments in early rheumatoid arthritis are common and lead to progressive deterioration of lower limb function. A gait rehabilitation programme underpinned by psychological techniques to improve adherence, may preserve gait and lower limb function. This study evaluated the feasibility of a novel gait rehabilitation intervention (GREAT Strides) and a future trial.MethodsThis was a mixed methods feasibility study with embedded qualitative components. People with early (< 2 years) rheumatoid arthritis (RA) and foot pain were eligible. Intervention acceptability was evaluated using a questionnaire. Adherence was evaluated using the Exercise Adherence Rating Scale (EARS). Safety was monitored using case report forms. Participants and therapists were interviewed to explore intervention acceptability. Deductive thematic analysis was applied using the Theoretical Framework of Acceptability. For fidelity, audio recordings of interventions sessions were assessed using the Motivational Interviewing Treatment Integrity (MITI) scale. Measurement properties of four candidate primary outcomes, rates of recruitment, attrition, and data completeness were evaluated.ResultsThirty-five participants (68.6% female) with median age (inter-quartile range [IQR]) 60.1 [49.4–68.4] years and disease duration 9.1 [4.0–16.2] months), were recruited and 23 (65.7%) completed 12-week follow-up. Intervention acceptability was excellent; 21/23 were confident that it could help and would recommend it; 22/23 indicated it made sense to them. Adherence was good, with a median [IQR] EARS score of 17/24 [12.5–22.5]. One serious adverse event that was unrelated to the study was reported. Twelve participants’ and 9 therapists’ interviews confirmed intervention acceptability, identified perceptions of benefit, but also highlighted some barriers to completion. Mean MITI scores for relational (4.38) and technical (4.19) aspects of motivational interviewing demonstrated good fidelity. The Foot Function Index disability subscale performed best in terms of theoretical consistency and was deemed most practical.ConclusionGREAT Strides was viewed as acceptable by patients and therapists, and we observed high intervention fidelity, good patient adherence, and no safety concerns. A future trial to test the additional benefit of GREAT Strides to usual care will benefit from amended eligibility criteria, refinement of the intervention and strategies to ensure higher follow-up rates. The Foot Function Index disability subscale was identified as the primary outcome for the future trial.Trial registrationISRCTN14277030
Trimeric complexes of Antp-TBP with TFIIEβ or Exd modulate transcriptional activity
Authors: Jiménez-Mejía Gustavo , Montalvo-Méndez Rubén , Hernández-Bautista Carolina , Altamirano-Torres Claudia , Vázquez Martha , Zurita Mario , Reséndez-Pérez Diana 
Published: May 2022

Abstract
Background
Hox proteins finely coordinate antero-posterior axis during embryonic development and through their action specific target genes are expressed at the right time and space to determine the embryo body plan. As master transcriptional regulators, Hox proteins recognize DNA through the homeodomain (HD) and interact with a multitude of proteins, including general transcription factors and other cofactors. HD binding specificity increases by protein–protein interactions with a diversity of cofactors that outline the Hox interactome and determine the transcriptional landscape of the selected target genes. All these interactions clearly demonstrate Hox-driven transcriptional regulation, but its precise mechanism remains to be elucidated.

Results
Here we report Antennapedia (Antp) Hox protein–protein interaction with the TATA-binding protein (TBP) and the formation of novel trimeric complexes with TFIIEβ and Extradenticle (Exd), as well as its participation in transcriptional regulation. Using Bimolecular Fluorescence Complementation (BiFC), we detected the interaction of Antp-TBP and, in combination with Förster Resonance Energy Transfer (BiFC-FRET), the formation of the trimeric complex with TFIIEβ and Exd in living cells. Mutational analysis showed that Antp interacts with TBP through their N-terminal polyglutamine-stretches. The trimeric complexes of Antp-TBP with TFIIEβ and Exd were validated using different Antp mutations to disrupt the trimeric complexes. Interestingly, the trimeric complex Antp-TBP-TFIIEβ significantly increased the transcriptional activity of Antp, whereas Exd diminished its transactivation.

Conclusions
Our findings provide important insights into the Antp interactome with the direct interaction of Antp with TBP and the two new trimeric complexes with TFIIEβ and Exd. These novel interactions open the possibility to analyze promoter function and gene expression to measure transcription factor binding dynamics at target sites throughout the genome.
Approach and solutions to congenital hearing impairment in Cameroon: perspective of hearing professionals
Authors: Choffor-Nchinda Emmanuel , Fokouo Fogha Jean Valentin , Ngo Nyeki Adèle-Rose , Dalil Asmaou Bouba , Meva’a Biouélé Roger Christian , Me-Meke Geschiere Peter 
Published: May 2022

Abstract
Objectives
To bring out the diagnostic attitude of hearing professionals in Cameroon towards congenital hearing impairment (CHI), assess availability of tests, neonatal screening, and create a national map of availability of treatment opportunities.

Methods
We conducted a cross-sectional online-based survey from June to December 2021, concerning ear–nose–throat (ENT) specialists, hearing care professionals, speech therapists and ENT nurses. A Google Forms online questionnaire was used to collect data, filled by eligible professionals involved in hearing care in Cameroon.

Results
A total of 93 professionals working in 31 different health facilities participated. A cumulative percentage of 79.9% of ENTs were found in just two out of 10 regions. Specialists sought by ENTs for assessment of patients with CHI included neurologists/neuro-pediatricians (96.8%), pediatricians (47.6%), other ENTs (34.9%), and psychologists (3.2%). Investigations requested included auditory-evoked brainstem response (ABR; 87.3%), otoacoustic emissions recording (OAE; 71.4%), and tympanometry (66.7%). There were eight OAE and nine ABR machines in the country. Twenty-five (88.6%) out of 31 facilities with otolaryngologists did not carry out systematic neonatal screening. Reasons included unavailability of equipment (21; 84%), and administrative delays (14; 56%). Sixteen (51.6%) facilities had ENTs with additional training in otologic surgery and 11 (35.5%) were equipped to perform ear surgery. Three centers (9.7%) specialized in hearing aid provision and maintenance services. Three hospitals (9.7%) had performed cochlear implantation.

Conclusion
Our results show scarcity and overt unevenness in distribution of specialists, equipment and solutions to CHI in Cameroon. A serious negative health care consequence of this shortage is the unavailability of universal newborn hearing screening and implementation programs.
Evaluation of mindfulness based stress reduction in symptomatic knee or hip osteoarthritis patients: a pilot randomized controlled trial
Authors: Marais Clémentine , Song Yujie , Ferreira Rosanna , Aounti Safa , Duflos Claire , Baptista Grégory , Pers Yves-Marie 
Published: May 2022

Abstract
Background
To evaluate the efficacy for symptomatic knee and hip osteoarthritis (OA) patients of a mindfulness-based stress reduction (MBSR) program versus usual care.

Methods
Randomized, physician-blind, clinical trial in a monocentric prospective pilot study. Adult participants with symptomatic knee or hip OA were randomized into either intervention or control groups. The intervention group completed the MBSR program for a two-and-a-half-hour weekly session for 8 weeks. Usual care management was similar in both groups. All patients were evaluated at baseline, 3 months and 6 months. The primary objective was to evaluate the change in WOMAC pain score between baseline and 3 months in the MBSR group compared to usual care group. Secondary objectives were to evaluate changes in pain VAS, WOMAC scores, quality of life (SF-36), HAD scores between baseline and 3/6 months.

Results
Forty patients were enrolled in the study. No differences in the WOMAC pain score between the two groups were observed in the different time points. A similar pattern was found for the other assessment outcomes. However, a significant pain VAS reduction in favor of the MBSR group between baseline and 6 months (− 29.6 ± 26.6 vs − 9.3 ± 27.3; p = 0.03) has been reached.

Conclusions
Our pilot RCT found contrasting results with no benefit on WOMAC pain and function and a delayed but long-term efficacy in pain VAS following a MBSR program in symptomatic knee or hip OA patients. Future studies with larger sample size are mandatory to confirm these preliminary results.
Trial registration The study was registered in ClinicalTrials.gov (NCT03644615, 23/08/2018).