bluuebunny/crossref_metadata_2025_split huggingface dataset:
Monte Carlo simulation method of polarization effects in Laser Compton Scattering on relativistic electrons
Authors: Filipescu Dan 
Published: November 2022

Abstract
Quasi-monochromatic, high energy and highly polarized γ-ray beam sources based on Compton scattering of laser photons (LCS) on relativistic electrons have developed for the last few decades as established instruments for nuclear physics studies. Following an extensive photoneutron experimental campaign at the LCS γ-ray beam line of the NewSUBARU synchrotron radiation facility at SPring8, Japan, a dedicated simulation code was developed for characterizing the incident γ-ray beams. The eliLaBr code is implemented using Geant4 and is available on the GitHub repository (github.com/dan-mihai-filipescu/eliLaBr). The present work describes step-by-step the Monte Carlo algorithm with focus on modeling the polarization properties of the scattered photon. The polarization is treated independently both in the Stokes parameters and in the polarization vector formalisms. An intervalidation between the two methods is given. Based on polarization state description requirements of different Geant4 physics classes, user recommendations are given on which of the two methods to be employed.

The spatial and energy distributions for the LCS γ-ray beam and its Stokes parameters are obtained for head-on laser — relativistic electron collisions, where several incident laser polarization states were considered: linear, unpolarized, circular and mixed linear and circular polarization. Results of previous investigations on the polarization of Compton scattered photons are reproduced.

The influence of variable incident angle between photon and electron beam was also investigated. We show that the degree of polarization transfer from the incident photon to the scattered photon increases with the collision angle, where head-on is considered 0°. However, as the polarization transfer is strongly influenced by the incident photon energy, we show that, for γ-ray sources based on Compton scattering of laser photons on relativistic electrons, the polarization degree of the incident photon is almost completely transferred to the scattered photon for any incident angle.
Translanguaging Practices in Content-based Instruction in L2 Arabic
Authors: Oraby Ebtissam , Azaz Mahmoud 
Published: November 2022

Abstract
Using the tenets of translanguaging and with a focus on Arabic as a diglossic language, we examine the fluid and dynamic practices that transcend the boundaries between/among Standard Arabic, Arabic dialects, and English in content-based instruction in an advanced Arabic literature course. Using conversation analysis, we show how translingual practices in learner–learner and teacher–learner interactions and discussions utilize the available linguistic repertoires in the classroom discourse. These practices broke the priori established boundaries that set Standard Arabic as the target language. The use of Arabic dialects and English in the literature course promoted the negotiation of complex concepts, facilitated the engagement with and critical interpretation of literary texts, and enhanced the meaning-making process at large. The utilization of these translingual practices has maximized Arabic learners’ gains. The article theoretically enriches recent discussions about the role of available linguistic repertoires in the ideological divide between language and content courses in language programs. It also advances the position that pedagogical translanguaging destabilizes the status of standard varieties as the target in diglossic languages.
Surgical resection rates after neoadjuvant therapy for localized pancreatic ductal adenocarcinoma: meta-analysis
Authors: Brown Zachary J , Heh Victor , Labiner Hanna E , Brock Guy N , Ejaz Aslam , Dillhoff Mary , Tsung Allan , Pawlik Timothy M , Cloyd Jordan M 
Published: November 2022

Abstract

Background
Neoadjuvant therapy is increasingly being used before surgery for localized pancreatic cancer. Given the importance of completing multimodal therapy, the aim of this study was to characterize surgical resection rates after neoadjuvant therapy as well as the reasons for, and long-term prognostic impact of, not undergoing resection.

Methods
A systematic review and meta-analysis of prospective trials and high-quality retrospective studies since 2010 was performed to calculate pooled resection rates using a generalized random-effects model for potentially resectable, borderline resectable, and locally advanced pancreatic cancer. Median survival times were calculated using random-effects models for patients who did and did not undergo resection.

Results
In 125 studies that met the inclusion criteria, neoadjuvant therapy consisted of chemotherapy (36.8 per cent), chemoradiation (15.2 per cent), or chemotherapy and radiation (48.0 per cent). Among 11 713 patients, the pooled resection rates were 77.4 (95 per cent c.i. 71.3 to 82.5), 60.6 (54.8 to 66.1), and 22.2 (16.7 to 29.0) per cent for potentially resectable, borderline resectable, and locally advanced pancreatic cancer respectively. The most common reasons for not undergoing resection were distant progression for resectable and borderline resectable cancers, and local unresectability for locally advanced disease. Among 42 studies with survival data available, achieving surgical resection after neoadjuvant therapy was associated with improved survival for patients with potentially resectable (median 38.5 versus 13.3 months), borderline resectable (32.3 versus 13.9 months), and locally advanced (30.0 versus 14.6 months) pancreatic cancer (P &lt; 0.001 for all).

Conclusion
Although rates of surgical resection after neoadjuvant therapy vary based on anatomical stage, surgery is associated with improved survival for all patients with localized pancreatic cancer. These pooled resection and survival rates may inform patient–provider decision-making and serve as important benchmarks for future prospective trials.
Mitochondrial haplogroups and cognitive progression in Parkinson’s disease
Authors: Liu Ganqiang , Ni Chunming , Zhan Jiamin , Li Weimin , Luo Junfeng , Liao Zhixiang , Locascio Joseph J , Xian Wenbiao , Chen Ling , Pei Zhong , Corvol Jean-Christophe , Maple-Grødem Jodi , Campbell Meghan C , Elbaz Alexis , Lesage Suzanne , Brice Alexis , Hung Albert Y , Schwarzschild Michael A , Hayes Michael T , Wills Anne-Marie , Ravina Bernard , Shoulson Ira , Taba Pille , Kõks Sulev , Beach Thomas G , Cormier-Dequaire Florence , Alves Guido , Tysnes Ole-Bjørn , Perlmutter Joel S , Heutink Peter , van Hilten Jacobus J , Barker Roger A , Williams-Gray Caroline H , Scherzer Clemens R ,   International Genetics of Parkinson Disease Progression (IGPP) Consortium, Liu Ganqiang , Valentino Rebecca R , Peng Jiajie , Liao Zhixiang , Locascio Joseph J , Corvol Jean-Christophe , Dong Xianjun , Maple-Grødem Jodi , Campbell Meghan C , Elbaz Alexis , Lesage Suzanne , Brice Alexis , Mangone Graziella , Growdon John H , Hung Albert Y , Schwarzchild Michael A , Hayes Michael T , Wills Anne-Marie , Herrington Todd M , Ravian Bernard , Shoulson Ira , Taba Pille , Kõks Sulev , Beach Thomas G , Cormier-Dequaire Florence , Alves Guido , Tysnes Ole-Bjørn , Perlmutter Joel S , Heutink Peter , van Hilten Jacobus J , Kasten Meike , Mollenhauer Brit , Trenkwalder Claudia , Klein Christine , Barker Roger A , Williams-Gray Caroline H , Marinus Johan , Scherzer Clemens R 
Published: November 2022

Abstract
Mitochondria are a culprit in the onset of Parkinson’s disease, but their role during disease progression is unclear. Here we used Cox proportional hazards models to exam the effect of variation in the mitochondrial genome on longitudinal cognitive and motor progression over time in 4064 patients with Parkinson’s disease. Mitochondrial macro-haplogroup was associated with reduced risk of cognitive disease progression in the discovery and replication population. In the combined analysis, patients with the super macro-haplogroup J, T, U# had a 41% lower risk of cognitive progression with P = 2.42 × 10−6 compared to those with macro-haplogroup H. Exploratory analysis indicated that the common mitochondrial DNA variant, m.2706A&gt;G, was associated with slower cognitive decline with a hazard ratio of 0.68 (95% confidence interval 0.56–0.81) and P = 2.46 × 10−5. Mitochondrial haplogroups were not appreciably linked to motor progression. This initial genetic survival study of the mitochondrial genome suggests that mitochondrial haplogroups may be associated with the pace of cognitive progression in Parkinson’s disease over time.
Inflammation as a chemoprevention target in asbestos-induced malignant mesothelioma
Authors: Kadariya Yuwaraj , Sementino Eleonora , Shrestha Ujjawal , Gorman Greg , White Jonathan M , Ross Eric A , Clapper Margie L , Neamati Nouri , Miller Mark Steven , Testa Joseph R 
Published: November 2022

Abstract
Malignant mesothelioma (MM) is an incurable cancer of the serosal lining that is often caused by exposure to asbestos. Therefore, novel agents for the prevention and treatment of this disease are urgently needed. Asbestos induces the release of pro-inflammatory cytokines such as IL-1β and IL-6, which play a role in MM development. IL-6 is a component of the JAK-STAT3 pathway that contributes to inflammation-associated tumorigenesis. Glycoprotein 130 (gp130), the signal transducer of this signaling axis, is an attractive drug target because of its role in promoting neoplasia via the activation of downstream STAT3 signaling. The anticancer drug, SC144, inhibits the interaction of gp130 with the IL-6 receptor (IL6R), effectively blunting signaling from this inflammatory axis. To test whether the inflammation-related release of IL-6 plays a role in the formation of MM, we evaluated the ability of SC144 to inhibit asbestos-induced carcinogenesis in a mouse model. The ability of sulindac and anakinra, an IL6R antagonist/positive control, to inhibit MM formation in this model was tested in parallel. Asbestos-exposed Nf2+/−;Cdkn2a+/− mice treated with SC144, sulindac or anakinra showed significantly prolonged survival compared to asbestos-exposed vehicle-treated mice. STAT3 activity was markedly decreased in MM specimens from SC144-treated mice. Furthermore, SC144 inhibited STAT3 activation by IL-6 in cultured normal mesothelial cells, and in vitro treatment of MM cells with SC144 markedly decreased the expression of STAT3 target genes. The emerging availability of newer, more potent SC144 analogs showing improved pharmacokinetic properties holds promise for future trials, benefitting individuals at high risk of this disease.
Embedding research ethics into an international development programme: a case study of Evidence and Collaboration for Inclusive Development (ECID) in Nigeria
Authors: Bollaert Cathy , Aliyu Talatu , Cascant-Sempere Ma Josep 
Published: November 2022

Abstract
This case study engages critically with the challenges of integrating research into an international development programme. Recognizing knowledge production is currently dominated by western and colonial systems of meaning–making, the case study also explores how development research can be less extractive and how it can promote more equitable forms of knowledge production. This is explored and illustrated through the ethical challenges raised in the Evidence and Collaboration for Inclusive Development (ECID) programme. This was a four-year programme, funded by the UK Government, and delivered through a consortium of nine partners led by Christian Aid, and implemented by in-country partner organizations in Myanmar, Nigeria and Zimbabwe during 2019–2021.
The article begins by contextualizing the ECID programme within the wider research environment and within the Nigerian country context (which is given particular focus). It then explores the ethical challenges that emerged from the programme and how these were addressed. The paper concludes by offering an innovative model for shifting power in development research and doing research ethically with communities in a development programme. This requires thinking about how ethics in development research and practice can be reviewed in organizations, which typically do not have their own ethics review boards, and in ways which do not reproduce western hegemony in relation to whose knowledge and ethics count in research practice.
Sleeve lobectomy in patients with non-small-cell lung cancer: a report from the European Society of Thoracic Surgery database 2021
Authors: Gonzalez Michel , Chriqui Louis-Emmanuel , Décaluwé Herbert , Aigner Clemens , Rényi-Vámos Ferenc , Opitz Isabelle , Furák József , Szanto Zalan , Brunelli Alessandro , Falcoz Pierre-Emmanuel 
Published: November 2022

Abstract

OBJECTIVES
For centrally located lung tumours, sleeve lobectomy is preferred over pneumectomy. We report on the surgical practices and perioperative outcomes of sleeve resections based on data from the European Society of Thoracic Surgeons database.

METHODS
We retrieved data of patients undergoing sleeve lobectomy or bilobectomy from 2007 to 2021. We evaluated baseline characteristics, surgical approach, neoadjuvant treatments, morbidity and postoperative outcomes of open and video-assisted thoracoscopic surgery (VATS) procedures.

RESULTS
In total, 1652 patients (median age: 63 years; females/males: 446/1206) underwent sleeve lobectomy (n = 1536) or bilobectomy (n = 116) by open thoracotomy (n = 1491; 90.2%) or VATS (n = 161; 9.8%) with a thoracotomy conversion rate of 21.1% (n = 34); 398 (24.1%) patients received neoadjuvant treatment. Overall morbidity and 30-day mortality were 40.6% and 2.2%, respectively. Bronchial anastomotic complications occurred in 29 patients (1.8%) with conservative treatment in 6 cases (20.7%) and operative management in 23 (79.3%). On multivariable analysis, factors related to the elevated risk of cardiopulmonary complications were body mass index &lt; 20 [odds ratio (OR): 2.26; P &lt; 0.001] and bilobectomy (OR : 2.28, P &lt; 0.001). Age &lt;60 years (OR: 0.71, P = 0.013), female sex (OR: 0.54, P &lt; 0.001) and VATS (0.64, P &lt; 0.001) were associated with decreased risk. Neoadjuvant treatment was not associated with increased risks of cardiopulmonary complications (OR: 1.05; P = 0.664). Compared to open thoracotomy, VATS was associated with significantly decreased overall morbidity (30.4% vs 41.7%, P = 0.006) and length of stay (median: 5 days vs 8 days; P &lt; 0.001).

CONCLUSIONS
Sleeve lobectomies can be safely performed after neoadjuvant treatment. The VATS approach fosters shorter length of stay and decreased morbidity.
Association of reproductive factors with cardiovascular disease risk in pre-menopausal women: nationwide population-based cohort study
Authors: Jeong Su-Min , Jeon Keun Hye , Jung Wonyoung , Yoo Jung Eun , Yoo Juhwan , Han Kyungdo , Kim Ju Youn , Lee Dong-Yun , Lee You-Bin , Shin Dong Wook 
Published: November 2022

Abstract

Background
Although the morbidity and mortality of cardiovascular diseases (CVD) are rising in young women, the risk factors of CVD among Korean pre-menopausal women have not been intensively investigated.

Aims
To determine how age at menarche and other female reproductive factors are associated with the risk of CVD in pre-menopausal women.

Methods and results
A total of 1 088 992 pre-menopausal women who participated in health screening in 2009 were included. The study outcomes were myocardial infarction (MI) and ischaemic stroke. Cox proportional hazards regression analysis was conducted with adjustment of traditional CVD risk factors and reproductive factors.

Results
Mean age was 43.8 ± 5.3 years (98.9%, &lt; 55 years), 3.5% were current smokers, and 1.2% were heavy drinkers. During a mean follow-up of 8.3years [9 032 685.9 person-years (PY)], there were 10 876 CVD events (1.0 per 1000 PY).With later menarche, the risk of CVD increased; ≤12 years [adjusted hazard ratio (HR) 1.04, 95% confidence interval 0.93–1.16], 13 years (reference), 14 years (1.06, 0.98–1.14), 15 years (1.15, 1.07–1.24), 16 years (1.23, 1.14–1.34), and ≥17 years (1.33, 1.24–1.44). Compared with non-users, oral contraceptives (OC) users (≥1 year) had an increased risk of CVD (1.11, 1.01–1.22) (P for trend = 0.007).

Conclusions
Later menarche than the mean age at menarche (13 years old) and the use of OC (≥1 year) were associated with a higher risk of CVD, after adjusting for traditional cardiovascular risk factors. This study suggests that female reproductive factors could be unique risk factors for CVD in pre-menopausal women.
Mycobacterium tuberculosis sRNA MTS2823 regulates the growth of the multidrug-resistant strain in macrophages
Authors: Chen Zhen , Jiang Wei , Zhang Mengli , Yu Bo , Li Wei , Liu Jijun , Ai Fen 
Published: November 2022

Abstract
Tuberculosis (TB), caused by Mycobacterium tuberculosis (MTB), is a serious contagious disease. MTB-encoded small regulatory RNA (sRNA) MTS2823 was reported to be upregulated in the plasma of TB patients. Nevertheless, whether MTS2823 is implicated in MTB drug resistance is unclear. Human macrophage cell line THP-1 was infected with the drug-susceptible strain H37Rv or the multidrug-resistant (MDR) strain 8462. Colony-forming unit assay was implemented for evaluating intracellular growth of the MTB strains. Enzyme-linked immunosorbent assay was used for measurement of inflammatory cytokines. Real-time quantitative polymerase chain reaction was utilized to assess MTS2823 and recombinase A (recA) expression in strains 8462 and H37Rv. Nitric oxide (NO) production in the MDR strain-infected THP-1 cells was measured. In this study, MTS2823 was found to display a low level in the MDR strain. Overexpressing MTS2823 promoted intracellular growth of the MDR strain and inhibited inflammatory cytokine and NO production in infected THP-1 cells. RecA might be a target of MTS2823 in the MDR strain. Overall, MTB-encoded sRNA MTS2823 displays a low level and regulates the growth of the MDR strain in THP-1 cells by modulating recA.
Multi-glycomic analysis of spheroid glycocalyx differentiates 2- and 3-dimensional cell models
Authors: Zhou Qingwen , Alvarez Michael Russelle S , Solakyildirim Kemal , Tena Jennyfer , Serrano Luster Mae N , Lam Matthew , Nguyen Cynthia , Tobias Fernando , Hummon Amanda B , Nacario Ruel C , Lebrilla Carlito B 
Published: November 2022

Abstract
A multi-glycomic method for characterizing the glycocalyx was employed to identify the difference between 2-dimensional (2D) and 3-dimensional (3D) culture models with two human colorectal cancer cell lines, HCT116 and HT29. 3D cell cultures are considered more representative of cancer due to their ability to mimic the microenvironment found in tumors. For this reason, they have become an important tool in cancer research. Cell–cell interactions increase in 3D models compared to 2D, indeed significant glycomic changes were observed for each cell line. Analyses included the N-glycome, O-glycome, glycolipidome, glycoproteome, and proteome providing the most extensive characterization of the glycocalyx between 3D and 2D thus far. The different glycoconjugates were affected in different ways. In the N-glycome, the 3D cells increased in high-mannose glycosylation and in core fucosylation. Glycolipids increased in sialylation. Specific glycoproteins were found to increase in the 3D cell, elucidating the pathways that are affected between the two models. The results show large structural and biological changes between the 2 models suggesting that the 2 are indeed very different potentially affecting individual outcomes in the study of diseases.
A neurodevelopmental disorder associated with an activatingde novomissense variant inARF1
Authors: Ishida Morié , Otero María G , Freeman Christina , Sánchez-Lara Pedro A , Guardia Carlos M , Pierson Tyler Mark , Bonifacino Juan S 
Published: November 2022

AbstractADP-ribosylation factor 1 (ARF1) is a small GTPase that regulates membrane traffic at the Golgi apparatus and endosomes through recruitment of several coat proteins and lipid-modifying enzymes. Here, we report a pediatric patient with an ARF1-related disorder because of a monoallelic de novo missense variant (c.296 G &gt; A; p.R99H) in the ARF1 gene, associated with developmental delay, hypotonia, intellectual disability and motor stereotypies. Neuroimaging revealed a hypoplastic corpus callosum and subcortical white matter abnormalities. Notably, this patient did not exhibit periventricular heterotopias previously observed in other patients with ARF1 variants (including p.R99H). Functional analysis of the R99H-ARF1 variant protein revealed that it was expressed at normal levels and properly localized to the Golgi apparatus; however, the expression of this variant caused swelling of the Golgi apparatus, increased the recruitment of coat proteins such as coat protein complex I, adaptor protein complex 1 and GGA3 and altered the morphology of recycling endosomes. In addition, we observed that the expression of R99H-ARF1 prevented dispersal of the Golgi apparatus by the ARF1-inhibitor brefeldin A. Finally, protein interaction analyses showed that R99H-ARF1 bound more tightly to the ARF1-effector GGA3 relative to wild-type ARF1. These properties were similar to those of the well-characterized constitutively active Q71L-ARF1 mutant, indicating that the pathogenetic mechanism of the R99H-ARF1 variant involves constitutive activation with resultant Golgi and endosomal alterations. The absence of periventricular nodular heterotopias in this R99H-ARF1 subject also indicates that this finding may not be a consistent phenotypic expression of all ARF1-related disorders.
Characterization of Classical Sheep Scrapie in White-tailed Deer after Experimental Oronasal Exposure
Authors: Greenlee Justin J , Moore S Jo , Cassmann Eric D , Lambert Zoe J , Kokemuller Robyn D , Smith Jodi D , Kunkle Robert A , Kong Qingzhong , Greenlee M Heather West 
Published: November 2022

Abstract

Background
Classic scrapie is a prion disease of sheep and goats that is associated with accumulation of abnormal prion protein (PrPSc) in the central nervous and lymphoid tissues. Chronic wasting disease (CWD) is the prion disease of cervids. This study was conducted to determine the susceptibility of white-tailed deer (WTD) to the classic scrapie agent.

Methods
We inoculated WTD (n = 5) by means of a concurrent oral/intranasal exposure with the classic scrapie agent from sheep or oronasally with the classic scrapie agent from goats (n = 6).

Results
All deer exposed to the agent of classic scrapie from sheep accumulated PrPSc. PrPSc was detected in lymphoid tissues at preclinical time points, and necropsies in deer 28 months after inoculation showed clinical signs, spongiform lesions, and widespread PrPSc in neural and lymphoid tissues. Western blots on samples from the brainstem, cerebellum, and lymph nodes of scrapie-infected WTD have a molecular profile similar to CWD and distinct from samples from the cerebral cortex, retina, or the original classic scrapie inoculum. There was no evidence of PrPSc in any of the WTD inoculated with classic scrapie prions from goats.

Conclusions
WTD are susceptible to the agent of classic scrapie from sheep, and differentiation from CWD may be difficult.