bluuebunny/crossref_metadata_2025_split huggingface dataset:
Large-Scale Proteomic Analysis of Soluble Compartment in Pediatric Acute Lymphoblastic Leukemia
Authors: Gentilcore Giusy , Deola Sara , Herrera Sheanna M , Lachica Che-Ann , Yousif Tayseer Abbas , Ahmed Areeg , Al Mulla Naima , Saleh Ayman , Mina Tommaso , Comoli Patrizia , Grivel Jean-Charles , Cugno Chiara 
Published: February 2021

Introduction
Acute Lymphoblastic Leukemia (ALL) is the most common malignancy in children and represents 75-80% of leukemia cases. Despite its recognized role in the initiation of the disease, the bone marrow (BM) microenvironment is not well understood especially in its non-cellular component.
High-throughput protein detection represent an opportunity to unveil new biomarkers for leukemia diagnosis, prognosis, monitoring, and to potentially identify biological targets.
Methods
In the present exploratory study, we evaluated the soluble compartment of BM and peripheral blood (PB) in 16 ALL pediatric patients by the means of the SOMAscan assay, a highly multiplexed, affinity proteomics platform able to measure 1305 proteins in as little as 65µl of sample using modified protein-binding single-stranded DNA aptamers called SOMAmers, revealed on a high dimension oligo-probe array. The raw hybridization data were normalized using hybridization controls and were log2-transformed. Transformed HybNormalized BM and PB plasma data were compared using GraphPad PRISM 8. Multiple comparisons were set with an FDR threshold of 0.01%.
Results
The comparative analysis between plasma samples from BM and PB showed that 228 proteins are differentially expressed in BM and PB plasma irrespective of the nature of disease (fig1). A more detailed mix-effect analysis of protein expression in the different patient categories and compartment defined in Table 1 revealed that out of these 228 proteins, 92 showed a significant differential expression when performing a mixed-effect analysis between the different groups. Among the top 20 proteins differentially expressed between BM and PB, 18 show differential expression between patient groups. The patient group effect is dominated by the differences between BM and PB plasma in ALL Common patients , which account for 17 of the observed differences in protein levels. In spite of the limited sample size, the analysis revealed a difference in NOTC2 level between ALL Common PB and ALL Pro-B PB.
Conclusion
In our study we applied a quantitative large-scale proteomic analysis on BM and PB plasma in children suffering from ALL, identifying differential protein expression between the two compartments.
In the last few years, SomaScan has emerged as a very attractive method due to its high throughput capacity, faster discovery mode compared to other proteomic platforms and small sample size required, which make it ideal for the identification of novel biomarkers. In spite of the limiting samples sizes, some differences in protein expression were revealed. We are taking this analysis further by analyzing more patients in different groups and including normal donor samples.
Table 1
Table

Disclosures
No relevant conflicts of interest to declare.
Magnetic Nanoparticles to Unique DNA Tracers: Effect of Functionalization on Physico-chemical Properties
Authors: Sharma Anuvansh , Foppen Jan Willem , Banerjee Abhishek , Sawssen Slimani , Bachhar Nirmalya , Peddis Davide , Bandyopadhyay Sulalit 
Published: February 2021

AbstractTo monitor and manage hydrological systems such as brooks, streams, rivers, the use of tracers is a well-established process. Limited number of potential tracers such as salts, isotopes and dyes, make study of hydrological processes a challenge. Traditional tracers find limited use due to lack of multiplexed, multipoint tracing and background noise, among others. In this regard, DNA based tracers possess remarkable advantages including, environmentally friendly, stability, and high sensitivity in addition to showing great potential in the synthesis of ideally unlimited number of unique tracers capable of multipoint tracing. To prevent unintentional losses in the environment during application and easy recovery for analysis, we hereby report DNA encapsulation in silica containing magnetic cores (iron oxide) of two different shapes—spheres and cubes. The iron oxide nanoparticles having size range 10–20 nm, have been synthesized using co-precipitation of iron salts or thermal decomposition of iron oleate precursor in the presence of oleic acid or sodium oleate. Physico-chemical properties such as size, zeta potential, magnetism etc. of the iron oxide nanoparticles have been optimized using different ligands for effective binding of dsDNA, followed by silanization. We report for the first time the effect of surface coating on the magnetic properties of the iron oxide nanoparticles at each stage of functionalization, culminating in silica shells. Efficiency of encapsulation of three different dsDNA molecules has been studied using quantitative polymerase chain reaction (qPCR). Our results show that our DNA based magnetic tracers are excellent candidates for hydrological monitoring with easy recoverability and high signal amplification.Graphic Abstract
Contribution of Small RNA Pathway to Interactions of Rice with Pathogens and Insect Pests
Authors: Feng Qin , Li Yan , Zhao Zhi-Xue , Wang Wen-Ming 
Published: February 2021

AbstractSmall RNAs (sRNAs) are mainly classified into microRNAs (miRNAs) and small interfering RNAs (siRNAs) according to their origin. miRNAs originate from single-stranded RNA precursors, whereas siRNAs originate from double-stranded RNA precursors that are synthesized by RNA-dependent RNA polymerases. Both of single-stranded and double-stranded RNA precursors are processed into sRNAs by Dicer-like proteins. Then, the sRNAs are loaded into ARGONAUTE proteins, forming RNA-induced silencing complexes (RISCs). The RISCs repress the expression of target genes with sequences complementary to the sRNAs through the cleavage of transcripts, the inhibition of translation or DNA methylation. Here, we summarize the recent progress of sRNA pathway in the interactions of rice with various parasitic organisms, including fungi, viruses, bacteria, as well as insects. Besides, we also discuss the hormone signal in sRNA pathway, and the emerging roles of circular RNAs and long non-coding RNAs in rice immunity. Obviously, small RNA pathway may act as a part of rice innate immunity to coordinate with growth and development.
Efficient Gene Stacking in Rice Using the GAANTRY System
Authors: Hathwaik Leyla T. , Horstman James , Thomson James G. , Thilmony Roger 
Published: February 2021

AbstractGenetic engineering of rice provides a means for improving rice grain quality and yield, and the introduction and expression of multiple genes can produce new traits that would otherwise be difficult to obtain through conventional breeding. GAANTRY (Gene Assembly in Agrobacterium by Nucleic acid Transfer using Recombinase technologY) was previously shown to be a precise and robust system to stably stack ten genes (28 kilobases (kb)) within an Agrobacterium virulence plasmid Transfer-DNA (T-DNA) and obtain high-quality Arabidopsis and potato transgenic events. To determine whether the GAANTRY system can be used to engineer a monocotyledonous crop, two new T-DNA constructs, carrying five (16.9 kb) or eleven (37.4 kb) cargo sequences were assembled and transformed into rice. Characterization of 53 independent transgenic events demonstrated that more than 50% of the plants carried all of the desired cargo sequences and exhibited the introduced traits. Additionally, more than 18% of the lines were high-quality events containing a single copy of the introduced transgenes and were free of sequences from outside of the T-DNA. Therefore, GAANTRY provides a simple, precise and versatile tool for transgene stacking in rice and potentially other cereal grain crops.
Evidence for multiple introductions of an invasive wild bee species currently under rapid range expansion in Europe
Authors: Lanner Julia , Gstöttenmayer Fabian , Curto Manuel , Geslin Benoît , Huchler Katharina , Orr Michael C. , Pachinger Bärbel , Sedivy Claudio , Meimberg Harald 
Published: February 2021

AbstractBackgroundInvasive species are increasingly driving biodiversity decline, and knowledge of colonization dynamics, including both drivers and dispersal modes, are important to prevent future invasions. The bee speciesMegachile sculpturalis(Hymenoptera: Megachilidae), native to East-Asia, was first recognized in Southeast-France in 2008, and has since spread throughout much of Europe. The spread is very fast, and colonization may result from multiple fronts.ResultTo track the history of this invasion, codominant markers were genotyped using Illumina sequencing and the invasion history and degree of connectivity between populations across the European invasion axis were investigated. Distinctive genetic clusters were detected with east–west differentiations in Middle-Europe.ConclusionWe hypothesize that the observed cluster formation resulted from multiple, independent introductions of the species to the European continent. This study draws a first picture of an early invasion stage of this wild bee and forms a foundation for further investigations, including studies of the species in their native Asian range and in the invaded range in North America.
The association between clinical laboratory data and chest CT findings explains disease severity in a large Italian cohort of COVID-19 patients
Authors:   on behalf of the Reggio Emilia COVID-19 Working Group;, Canovi Simone , Besutti Giulia , Bonelli Efrem , Iotti Valentina , Ottone Marta , Albertazzi Laura , Zerbini Alessandro , Pattacini Pierpaolo , Giorgi Rossi Paolo , Colla Rossana , Fasano Tommaso 
Published: February 2021

Abstract
Background
Laboratory data and computed tomography (CT) have been used during the COVID-19 pandemic, mainly to determine patient prognosis and guide clinical management. The aim of this study was to evaluate the association between CT findings and laboratory data in a cohort of COVID-19 patients.

Methods
This was an observational cross-sectional study including consecutive patients presenting to the Reggio Emilia (Italy) province emergency rooms for suspected COVID-19 for one month during the outbreak peak, who underwent chest CT scan and laboratory testing at presentation and resulted positive for SARS-CoV-2.

Results
Included were 866 patients. Total leukocytes, neutrophils, C-reactive protein (CRP), creatinine, AST, ALT and LDH increase with worsening parenchymal involvement; an increase in platelets was appreciable with the highest burden of lung involvement. A decrease in lymphocyte counts paralleled worsening parenchymal extension, along with reduced arterial oxygen partial pressure and saturation. After correcting for parenchymal extension, ground-glass opacities were associated with reduced platelets and increased procalcitonin, consolidation with increased CRP and reduced oxygen saturation.

Conclusions
Pulmonary lesions induced by SARS-CoV-2 infection were associated with raised inflammatory response, impaired gas exchange and end-organ damage. These data suggest that lung lesions probably exert a central role in COVID-19 pathogenesis and clinical presentation.
One year of procarbazine lomustine and vincristine is poorly tolerated in low grade glioma: a real world experience in a national neuro-oncology centre
Authors: Keogh Rachel J. , Aslam Razia , Hennessy Maeve A. , Coyne Zac , Hennessy Bryan T. , Breathnach Oscar S. , Grogan Liam , Morris Patrick G. 
Published: February 2021

Abstract
Background
Following optimal local therapy, adjuvant Procarbazine, Lomustine and Vincristine (PCV) improves overall survival (OS) in low-grade glioma (LGG). However, 1 year of PCV is associated with significant toxicities. In the pivotal RTOG 9802 randomised control trial, approximately half of the patients discontinued treatment after 6 months. As patients on clinical trials may be fitter, we aimed to further explore the tolerability of PCV chemotherapy in routine clinical practice.

Methods
We conducted a retrospective study between 2014 and 2018 at a National Neuro-Oncology centre. Patients who had received PCV during this time period were included. The primary objective was to assess tolerability of treatment. Secondary objectives included evaluation of treatment delays, dose modifications and toxicities.

Results
Overall, 41 patients were included, 24 (58%) were male and 21 (51%) aged ≥40 years. 38 (93%) underwent surgical resection and all patients received adjuvant radiotherapy prior to chemotherapy. The median number of cycles completed was 3,2,4 for procarbazine, lomustine and vincristine respectively. Only 4 (10%) completed all 6 cycles of PCV without dose modifications. There was a universal decline in dose intensity as cycles of chemotherapy progressed. Dose intensity for cycle 1 versus cycle 6 respectively: procarbazine (98% versus 46%), lomustine (94% versus 48%) and vincristine (93% versus 50%). Haematological toxicities were common. Six (14%) patients experienced Grade III-IV thrombocytopaenia and 13 (31%) experienced Grade III-IV neutropaenia.

Conclusion
Toxicities are frequently observed with the PCV regimen in clinical practice. It might be preferable to adjust doses from the start of chemotherapy to improve tolerability or consider alternative chemotherapy, particularly in older patients with LGG.
Nd:YAG capsulotomy for Ahmed glaucoma drainage implant occlusion by the anterior capsule: a case report
Authors: Ertel Monica Kenney , Gelinas Nathaniel Ryan , Slingsby Taylor John , Seibold Leonard Keith , Kahook Malik Yaser , SooHoo Jeffrey Raymond 
Published: February 2021

AbstractBackgroundGlaucoma drainage implants have been used with increasing frequency for the management of glaucoma. Patients who are candidates for glaucoma drainage devices often have more severe disease and are at risk of vision loss with post-operative elevations in intraocular pressure (IOP). One post-operative complication that can result in IOP elevation after glaucoma drainage device implantation is occlusion of the tube lumen.Case presentationHere, we present a novel case of tube occlusion by the anterior capsule in a patient who underwent combined phacoemulsification and Ahmed glaucoma valve implantation. The tube occlusion was successfully managed with Nd:YAG capsulotomy with immediate IOP lowering.ConclusionsWhile there have been previous reports of occlusion of the tube lumen by vitreous, iris, blood and fibrin, to our knowledge this is the first report of tube occlusion by the anterior lens capsule and the first report to describe its successful management.
Four mutations in MITF, SOX10 and PAX3 genes were identified as genetic causes of waardenburg syndrome in four unrelated Iranian patients: case report
Authors: Zardadi Safoura , Rayat Sima , Doabsari Maryam Hassani , Alishiri Aliagha , Keramatipour Mohammad , Shahri Zeynab Javanfekr , Morovvati Saeid 
Published: February 2021

Abstract
Background
Waardenburg syndrome (WS) is a rare genetic disorder. The purpose of this study was to investigate clinical and molecular characteristics of WS in four probands from four different Iranian families.

Case presentation
The first patient was a 1-year-old symptomatic boy with congenital hearing loss and heterochromia iridis with a blue segment in his left iris. The second case was a 1.5-year-old symptomatic girl who manifested congenital profound hearing loss, brilliant blue eyes, and skin hypopigmentation on the abdominal region at birth time. The third patient was an 8-month-old symptomatic boy with developmental delay, mild atrophy, hypotonia, brilliant blue eyes, skin hypopigmentation on her hand and foot, Hirschsprung disease, and congenital profound hearing loss; the fourth patient was a 4-year-old symptomatic boy who showed dystopia canthorum, broad nasal root, synophrys, skin hypopigmentation on her hand and abdomen, brilliant blue eyes, and congenital profound hearing loss. Whole exome sequencing (WES) was used for each proband to identify the underlying genetic factor. Sanger sequencing was performed for validation of the identified mutations in probands and the available family members. A novel heterozygous frameshift mutation, c.996delT (p.K334Sfs*15), on exon 8 of the MITF gene was identified in the patient of the first family diagnosed with WS2A. Two novel de novo heterozygous mutations including a missense mutation, c.950G > A (p.R317K), on exon 8 of the MITF gene, and a frameshift mutation, c.684delC (p.E229Sfs*57), on the exon 3 of the SOX10 gene were detected in patients of the second and third families with WS2A and PCWH (Peripheral demyelinating neuropathy, Central dysmyelinating leukodystrophy, Waardenburg syndrome, Hirschsprung disease), respectively. A previously reported heterozygous frameshift mutation, c.1024_1040del AGCACGATTCCTTCCAA, (p.S342Pfs*62), on exon 7 of the PAX3 gene was identified in the patient of the fourth family with WS1.

Conclusions
An exact description of the mutations responsible for WS provides useful information to explain the molecular cause of clinical features of WS and contributes to better genetic counseling of WS patients and their families.
Posttraumatic stress disorder among adolescents in Brazil: a cross-sectional study
Authors: Avanci Joviana Quintes , Serpeloni Fernanda , de Oliveira Thiago Pires , de Assis Simone Gonçalves 
Published: February 2021

Abstract
Background
The frequency of trauma and different types of violence exposure in urban areas and their effects on the mental health of adolescents in developing countries are poorly investigated. Most information about traumatized young people comes from war scenarios or disasters. This study aimed to determine the prevalence of PTSD in trauma-exposed students in a low-resource city of the state of Rio de Janeiro, Brazil. The effects of sociodemographic and individual and family factors in the development of PTSD were also investigated.

Methods
Through multi-stage cluster sampling, 862 adolescents (Mage = 15 years old, 65% female) from public and private schools in the city of São Gonçalo were selected for the study. Self-rating structured questionnaires were applied to assess sociodemographic profile, exposure to physical and psychological violence (family, school, community), sexual abuse, social support, social functional impairment, resilience, and posttraumatic stress disorder. The data were grouped in blocks regarding sociodemographic, individual, family, and community variables. For statistical analysis, chi-square, Fisher’s exact test, and logistic regression were performed.

Results
The PTSD prevalence was 7.8% among adolescents. Boys were exposed to significantly higher number of events of community violence, while girls to family violence. The adjusted odds ratio (OR) for PTSD were statistically significant for age (OR, 1.45, [95% CI, 1.043–2.007]), social functional impairment (OR, 4.82, [95% CI, 1.77–13.10]), severe maternal physical violence (OR, 2.79, [95% CI, 0.79–9.93]), psychological violence by significant people (OR, 3.96, [95% CI, 1.89–8.31]) and a high number of episodes of community violence (OR, 3.52, [95% CI, 1.47–8.40).

Conclusions
There was a high prevalence of PTSD within this population associated with exposure to violence. Not only physical, but also psychological violence contributed to PTSD. The results also raise awareness to the differences in life trajectories between boys and girls regarding violence. These differences need to be better understood in order to enable the development of effective preventative interventions. Treating and preventing mental health disorders presents a challenge for countries, especially those with a lower degree of social and economic development and high community violence.
Dysplasia epiphysealis hemimelica of the radial head: a rare case report
Authors: Mohamadian Hiva , Bahardoust Mansour , Sanandaji Borzouyeh Molazem , Saberi Saba 
Published: February 2021

Abstract
Background
Dysplasia epiphysealis hemimelica (DEH) is a rare benign overgrowth generally affecting the epiphyses and short bones of the lower limbs. DEH in the elbow joint is extremely rare, and to date, only three cases of DEH have been reported in the radial head.

Case presentation
In this study, we report a case of DEH located in the radial head of the right elbow of a 10-year-old boy, which was presented with elbow pain and limited range of motion. In clinical examination, an asymmetrical enlargement was observed over the elbow. The lesion was resected surgically, and the patient’s symptoms resolved afterward. The histologic analysis of the lesion confirmed the diagnosis of DEH.

Conclusion
This report highlights the role of DEH in the differential diagnosis of elbow pathologies, particularly its differentiation from osteochondroma.
Utilising the perspectives of patients with lower-limb osteoarthritis on prescribed physical activity to develop a theoretically informed physiotherapy intervention
Authors: Willett Matthew , Greig Carolyn , Fenton Sally , Rogers David , Duda Joan , Rushton Alison 
Published: February 2021

Abstract
Background
Lower-limb osteoarthritis (OA) causes high levels of pain and disability. Physiotherapists are the primary healthcare provider of non-pharmacological treatments, and incorporate strategies to optimise physical activity (PA) to aid patients with lower-limb OA to moderate their clinical symptoms. However, patients with lower-limb OA have low adherence to PA recommendations both during treatment and after discharge. This study aimed to use knowledge of identified barriers and facilitators to physiotherapy prescribed PA (during treatment and post-discharge) to develop a theoretically informed intervention to optimise adherence to PA for patients with lower-limb OA during treatment and post-discharge.

Methods
1) A purposive sample of 13 patients with lower-limb OA participated in semi-structured interviews following physiotherapy treatment. Inductive analysis identified themes/subthemes reflecting barriers and facilitators to physiotherapist prescribed PA, which were organised deductively according to personal factors, treatment and post-discharge phases.
2) Themes/subthemes were mapped onto the theoretical domains framework (TDF).
3) Behaviour change techniques (BCTs) were coded from the key identified domains and a theoretically informed physiotherapy intervention addressing barriers and using facilitators, was developed.

Results
Themes of patient confidence, mind-set, motivation, OA symptoms and PA experiences were primary personal factors that influenced PA adherence; with the TDF domain ‘Beliefs about capabilities’ most important to target. During treatment, the theme of routine formation was the major driver of personal factors; and primarily influenced by developing a positive physiotherapist-patient relationship. Post-discharge, physical factors, psychosocial factors and ongoing access to resources were important themes influencing PA maintenance. ‘Environmental context and resources’ and ‘social influences’ emerged as the key TDF domains to target during treatment and post-discharge. The proposed theoretically informed intervention included 26 BCTs delivered across conceptual phases of adoption, routine formation, and maintenance.

Conclusion
A theoretically informed physiotherapy intervention was proposed to optimise PA adherence in patients with lower-limb OA. The included BCTs primarily target patients’ perceived beliefs about their capabilities, by developing a PA routine during treatment and facilitating appropriate psychosocial support and access to resources for PA maintenance post-discharge. The feasibility of delivering the intervention in clinical practice will now be evaluated.